Download - ARC Centre of Excellence for Coral Reef Studies

Cover Photo and above © Giles Winstanley / pelagicon.com2009

Director’s ReportWelcome to our 2009 annual report. A keyoutcome for the year has been our commitmentto organize and host the next InternationalCoral Reef Symposium (ICRS) in Australia.Almost 3000 delegates attended the 11th ICRSin Fort Lauderdale, Florida, in 2008. The ICRSis the world’s largest and premier forum forthe dissemination and discussion of coral reefscience, management and conservation. TheARC Centre made a major contribution to the11th symposium, presenting 124 talks andposters during the 5-day event. We look forwardto co-hosting the 12th ICRS with James CookUniversity in the tropical city of Cairns in July2012 (see p.47).The Centre’s publication output continued togrow rapidly this year, doubling since 2006. Our224 publications in 2009 were co-authored bycolleagues from 345 institutions in 52 countries,reflecting our extensive activities around theworld. Among this year’s publications is aprovocative multi-national study on planetarytipping points published in Nature, and a PolicyForum article in Science magazine on missinginstitutions for coping with trans-boundary issuessuch as climate change and oceanic fisheries(see p.24). These trans-disciplinary studies willbe developed further by research programs 5, 6and 7 in 2010. A new ISI Web of Science analysisof journal publications and citations identifies ourARC Centre of Excellence as the premier climatechange research institution in Australia, withJames Cook University ranked 2nd in the worldfor citation impact (p.54).The ARC Centre’s fieldwork in 2009 wasundertaken in 23 tropical countries, with a majorongoing focus in the Coral Triangle region to thenorth of Australia. The Centre expended over$3 million this past year to support fieldworkin the Philippines, Indonesia, Papua NewGuinea and the Solomon Islands. Our websitefeatures a new list of links to 134 of the Centre’spublications featuring science undertaken withinthe Coral Triangle (www.coralcoe.org.au/events/ctiworkshop/pubscticountry10.pdf). In May,we provided expertise and advice at the WorldOcean Conference in Manado, Indonesia, wherethe six Coral Triangle nations launched an accordfor sustainable management of coral reefsacross the region. During the year, the Centreprovided briefings in Townsville on Coral Triangleresearch and on our capacity-building activitiesto the Ambassadors and Consular Generals ofIndonesia, Papua New Guinea, the SolomonIslands, Timor-Leste, and the USA.We’ve had a very busy year providing adviceand services to governments, agencies and NonGovernment Organisations (NGOs) around theworld. In February, Deputy Director MalcolmMcCulloch and I joined colleagues from NationalAcademies of Australia and nine other countriesto write an Inter-Academy statement on oceanacidification. The statement, timed in advanceof the Copenhagen United Nations FrameworkConvention on Climate Change (UNFCCC)negotiations, summarizes the current state of thescience, and is aimed at policy-makers. Deputy-Director Ove Hoegh-Guldberg was involved inIntergovernmental Panel on Climate Change(IPCC) workshops in Venice and Geneva, andprovided UNFCCC briefings in Barcelona andCanberra. In September, I delivered a plenarytalk in Stockholm, at an international conferenceof environmental policy-makers, held underthe auspices of the Swedish Presidency of theEuropean Union. In Australia, Centre membersdrafted sections of the national Climate ChangeResearch Plan for marine biodiversity andresources. The Plan provides a framework toguide research funding decisions for developingeffective adaptation strategies. In November,4ARC Centre of Excellence for Coral Reef Studies

Management StructureCentre Advisory BoardScientific ManagementCommitteeCentre DirectorProfessor Terry HughesBusiness TeamAssistant DirectorDavid YellowleesChief Operations OfficerJennifer LappinFinance Manager &Student CoordinatorOlga BazakaOffice ManagerMonica GaffneyAdministrative OfficerJanet SwansonConference CoordinatorEliza GlassonProgram 1Program 2Program 3Program 4EvolutionaryandEnvironmentalChangeUnderstandingand ManagingCoral ReefBiodiversityMarineReserves andConnectivityGarry RussGenetic,Molecular andPhysiologicalProcessesMalcolm McCullochSean ConnollyOve Hoegh-GuldbergProgram 5Program 6Program 7Program 8Resilience ofLinked Social-EcologicalSystemsTerry HughesConservationPlanning for aSustainableFutureBob PresseyPolicyDevelopment,Institutions andGovernance ofCoral ReefsSimon FoaleGenomics andMetagenomicsof Coral ReefsDavid Miller6ARC Centre of Excellence for Coral Reef Studies

GovernanceThe Centre’s governance structuresinvolve stakeholders in planningand management processes. Thechart opposite illustrates the currentgovernance structure and relationships.Programs 7 and 8 commenced during2009 and the Centre’s governancestructures were revised to incorporatethese two new research programs.James Cook University is theadministering organisation withthe Centre Director, Terry Hughesreporting to Professor Chris Cocklin,the Deputy Vice-Chancellor (Researchand Innovation). The Centre’s ChiefInvestigators are located in threeFaculties at JCU, and at the AustralianNational University, the Universityof Queensland and the University ofWestern Australia which joined theCentre this year. Partner Investigatorsare based at the Australian Institute ofMarine Science, the Great Barrier ReefMarine Park Authority, and in overseasinstitutions. Day-to-day operationsare managed by the Chief OperationsOfficer, Jenny Lappin, in consultationwith the Centre Director and AssistantDirector, David Yellowlees. The CentreDirector oversees the Centre’s researchprograms together with the two deputydirectors, Ove Hoegh-Guldberg (UQ) andMalcolm McCulloch (UWA).Centre Advisory BoardThe ARC Centre’s Advisory Boardprovides vision and strategic adviceand facilitates improved linkagesbetween the Centre and the privatesector, government agencies, researchinstitutions and the wider community.From 2010 the focus of the Board willbe more global, reflecting the Centre’sincreasing international engagement. TheCentre Director and Chief OperationsOfficer provide the operational andmanagement link between the AdvisoryBoard and the Centre. The Board metformally in Canberra in April 2009.In 2009, the ARC Centre of ExcellenceReview Panel recommended that theCentre vary the representation of itsAdvisory Board to match the Centre’sdemonstrably strong global researchactivities and international linkages. Inconjunction with this change to AdvisoryBoard membership, the Review Panelalso recommended that the terms ofreference for the Board be revised totake account of the Centre’s internationalprofile and its focus on sustainablemanagement of coral reefs. In responseto this, the terms of reference of theAdvisory Board have been updated,and several new members have beenrecruited for next year. The first meetingof the new board will be in March 2010.We have been privileged to haveaccess to the expertise and experienceof our departing university Boardmembers and would like to thankProfessors Chris Cocklin, Max Luand Mandy Thomas for their adviceand contribution to the Centre.In 2009, the Advisory Board’smembership was:Dennis Trewin (Chair)former Australian StatisticianProfessor Chris CocklinDeputy Vice-Chancellor(Research and Innovation)James Cook UniversityProfessor Max LuDeputy Vice Chancellor (Research)University of QueenslandProfessor Mandy ThomasPro Vice-ChancellorAustralian National UniversityDr Ian PoinerChief Executive OfficerAustralian Institute of Marine ScienceAndrew SkeatGeneral ManagerGreat Barrier Reef Marine Park AuthorityHonourable Virginia Chadwickformer ChairGreat Barrier Reef Marine Park AuthorityProfessor Terry HughesARC Centre Directorand Federation FellowScientific ManagementCommitteeOngoing operational management ofthe Centre and planning for its scientificresearch program is the responsibility ofthe Scientific Management Committee(SMC). The SMC is chaired by aneminent Israeli researcher, ProfessorYossi Loya. Other members are theleaders of each of the Centre’s eightResearch Programs, and the Directorof the Knowledge Management Groupfrom the Great Barrier Reef MarinePark Authority, the Centre’s principalend-user in Australia. Priorities foreach meeting include reviewing andexpanding the objectives and operationsfor the Centre’s research programs,developing international collaborationsand engagements, recruiting high-2009 annual report 7

Governancequality postdoctoral fellows, planningprofessional development programs,undertaking an effective communicationsstrategy and reviewing processes forengaging with the Centre’s many endusersaround the world. The Committeemet 3 times in 2009, in February(videoconference), April (Townsville) andOctober (Israel).Priorities for the SMC in 2009 includedresponding to the ARC review, continuingto expand the Centre’s internationalengagement, particularly in the CoralTriangle region, developing the Centre’soutreach program and respondingto the Australian Government’s newresearch fellowship initiatives. Thetrans-disciplinary nature of the Centre’sresearch was further developed during2009 with the establishment of twonew research programs: Program7: Policy development, institutionsand governance of coral reefs (seep.28) and Program 8: Genomics andmetagenomics of coral reefs (see p.30).Scientific Management CommitteeMembers are:Professor Yossi Loya (Chair)Professor of Marine BiologyThe Raynor Chair for EnvironmentalConservation ResearchTel Aviv UniversityIsraelDr David WachenfeldDirector, Knowledge Management GroupGreat Barrier Reef Marine Park AuthorityProfessor Malcolm McCullochLeader, Research Program 1University of Western AustraliaProfessor Sean ConnollyLeader, Research Program 2James Cook UniversityProfessor Garry RussLeader, Research Program 3James Cook UniversityProfessor Ove Hoegh-GuldbergLeader, Research Program 4University of QueenslandProfessor Terry HughesLeader, Research Program 5James Cook UniversityProfessor Bob PresseyLeader, Research Program 6James Cook UniversityDr Simon FoaleLeader, Research Program 7James Cook UniversityProfessor David MillerLeader, Research Program 8James Cook University8ARC Centre of Excellence for Coral Reef Studies

HonourableVirginia Chadwick1944 – 2009Sadly, Virginia Chadwick died on 19thSeptember 2009 after a long anddetermined battle with cancer. Shewas a supporter of the ARC Centrefrom its inception, commencing withan enthusiastic letter of support for ourinitial application in 2004. As Chair of theGreat Barrier Reef Marine Park Authority(GBRMPA), she became an AdvisoryBoard member of the ARC Centre onits establishment in mid 2005 and wasa major contributor to the strategicdirection of the Centre. She remained asa Board member following her retirementand relocation to NSW. Her insight intohow the ARC Centre could contributeto management of coral reefs and topolicy was invaluable in the Centre’ssuccess. Her significant contribution wasrecognized by James Cook Universityby the award of an Honorary Doctorate,which she received in a ceremony inTownsville on 28th March 2009. Hercounsel and support will be sorelymissed within the ARC Centre. InVirginia’s honour the Centre of Excellencehas established “The Virginia ChadwickAwards”, in recognition each year of fiveoutstanding publications written by ARCCentre of Excellence graduate students.Virginia Chadwick served the peopleof Queensland and Australia withdistinction through her contribution toconserving the marine environment, asChair and CEO of the Great Barrier ReefMarine Park Authority (1999 – 2007).Before moving to Townsville, she hada distinguished political career in NewSouth Wales, including a term as theState’s Education Minister.Upon taking up the position, Virginialed The Authority in a visionary plan toenhance the level of protection for theGreat Barrier Reef - The Great BarrierReef Marine Park Representative AreasProgram (RAP). This program has beenthe most comprehensive and innovativemarine conservation and biodiversityprogram ever to occur in worldmarine conservation. The program willsignificantly enhance the resilience of theGreat Barrier Reef (GBR) in the face ofmounting environmental pressures, andwill assist industry, particularly tourismand fisheries, to achieve increased levelsof environmental sustainability andfinancial security.The Great Barrier Reef Marine ParkZoning Plan, the statutory instrumentgiving effect to the RepresentativeAreas Program, was tabled in FederalParliament on 3 December 2003, andpassed through all legislative stagesduring early 2004. The Zoning Plan tookeffect on 1 July 2004.Under Virginia Chadwick’s direction andleadership, officers of the GBRMPAconvened panels of independent naturaland social scientists. Their aim was todevelop planning principles on how tobest protect the reef, while minimisingimpacts for those who depend on thereef for their livelihood. After arrangingfor peer review of the principles, Virginiadirected a major program of bioregionalmapping for the GBR, using the bestscientific advice, and ground-breakingapplied spatial data technology.In 2002, Virginia Chadwick and herteam directed and conducted the mostextensive community consultationprocess ever conducted in Australia. Thefirst phase of community consultationwith stakeholders and local communitiesin Queensland involved hundreds ofmeetings with thousands of peoplein coastal Queensland. Over 10,500submissions were received as a resultof phase 1 and a further 20,000 in phase2. The result was the issue of the GreatBarrier Reef Marine Park Zoning Plan,which has minimized, as far as possible,impacts on users of the Marine Park,while maximizing the level of biodiversityprotection. Because of the level of cooperationfrom local communities, theGBRMPA has been able to access localknowledge, and significantly reduceimpacts on existing users.The success of this very sizeableconsultation process, and the timelytabling of the Zoning Plan in December2003, was due substantially to theoutstanding professional and personalcontribution made by Virginia.These works have made a verysignificant contribution to fosteringinternational awareness of sophisticatedenvironmental conservation initiatives,and have served to enhance Australia’sinternational marine conservationreputation. The RAP initiative has beenrecognized by nine major awards - threeinternational and six national - and seta new global benchmark for marineconservation. This outcome would nothave been possible without Virginia’sdrive and vision.2009 annual report 9

membershipResearchersProfessor Terry HughesCentre Director and ARC FederationFellow, Program 5 leaderJames Cook UniversityDr Tracy AinsworthARC Australian Postdoctoral FellowJames Cook UniversityDr Glenn AlmanyARC Future FellowJames Cook UniversityDr Kenneth AnthonyChief InvestigatorUniversity of QueenslandDr Andrew BairdARC Future FellowJames Cook UniversityDr Natalie BanARC Australian Postdoctoral FellowJames Cook UniversityDr Line BayQueensland Smart State FellowJames Cook UniversityProfessor David BellwoodChief InvestigatorJames Cook UniversityDr Joshua CinnerARC Australian Postdoctoral FellowJames Cook UniversityProfessor Sean ConnollyARC Australian Professorial Fellowand Program 2 leaderJames Cook UniversityDebora De FreitasResearch AssociateJames Cook UniversityDr Guillermo Diaz-PulidoResearch FellowUniversity of QueenslandDr Maria DornelasResearch FellowJames Cook UniversityAssociate Professor Sophie DoveChief InvestigatorUniversity of QueenslandDr Simon DunnResearch FellowUniversity of QueenslandDr Toby ElmhirstResearch FellowJames Cook UniversityDr Kathryn FergusonARC Australian Postdoctoral FellowJames Cook UniversityDr Pedro FidelmanResearch FellowJames Cook UniversityDr Simon FoaleResearch Fellow and Program 7 LeaderJames Cook UniversityProfessor Carl FolkePartner InvestigatorStockholm UniversityDr Sylvain ForêtResearch FellowJames Cook UniversityDr Christopher FultonChief InvestigatorAustralian National UniversityDr Nick GrahamARC Australian Postdoctoral Fellowand Queensland Smart Futures FellowJames Cook UniversityDr Lauretta GrassoResearch AssociateJames Cook UniversityProfessor Ove Hoegh-GuldbergDeputy Director, Queensland SmartState Premier’s Fellowand Program 4 LeaderUniversity of QueenslandProfessor Geoffrey JonesChief InvestigatorJames Cook UniversityProfessor Ronald KarlsonPartner InvestigatorUniversity of DelawareProfessor Michael KingsfordChief InvestigatorJames Cook UniversityDr Johnathan KoolResearch FellowJames Cook UniversityDr Bill LeggatChief InvestigatorJames Cook UniversityDr Janice LoughPartner InvestigatorAustralian Institute of Marine ScienceDr Jennie MallelaResearch FellowAustralian National UniversityDr Laurence McCookPartner InvestigatorGreat Barrier Reef Marine Park AuthorityDr Mark McCormickChief InvestigatorJames Cook UniversityProfessor Malcolm McCullochDeputy Director, Western AustraliaPremier’s Fellow and Program 1 LeaderUniversity of Western AustraliaDr Mark MeekanPartner InvestigatorAustralian Institute of Marine ScienceProfessor David MillerChief Investigator and Program 8 LeaderJames Cook UniversityProfessor Philip MundayARC Queen Elizabeth II FellowJames Cook UniversityProfessor John PandolfiChief InvestigatorUniversity of QueenslandDr Serge PlanesPartner InvestigatorUniversity of PerpignanDr Morgan PratchettARC Australian Research FellowJames Cook UniversityProfessor Bob PresseyResearch Fellow and Program 6 LeaderJames Cook UniversityProfessor Garry RussChief Investigator and Program 3 LeaderJames Cook University10ARC Centre of Excellence for Coral Reef Studies

Professor Robert SteneckPartner InvestigatorUniversity of MaineDr Madeleine van OppenPartner InvestigatorAustralian Institute of Marine ScienceDr Benjamin WaltherResearch FellowAustralian National UniversityDr David WilliamsonResearch FellowJames Cook UniversityProfessor Bette WillisChief InvestigatorJames Cook UniversityProfessor David YellowleesChief InvestigatorJames Cook UniversityResident InternationalScholarsDr Tatjana GoodSwiss National Foundation, SwitzerlandDr Cristina LinaresUniversity of Barcelona, SpainProfessor Yossi LoyaTel Aviv University, IsraelDr Aurélie MoyaMarie Curie FellowUniversity of Nice, FranceDr Lucie PeninMarie Curie FellowUniversity of Perpignan, FranceAdjunct ResearchersDr Alison GreenThe Nature ConservancyDr Alexander KerrUniversity of Guam, USAProfessor Janice LoughAustralian Institute of Marine ScienceProfessor Yossi LoyaTel Aviv University, IsraelDr Tim LynamCSIRODr Laurence McCookGreat Barrier Reef Marine Park AuthorityDr Madeleine van OppenAustralian Institute of Marine ScienceProfessor John TanzerEnvironmental Pathways and SolutionsDr David WachenfeldGreat Barrier Reef Marine Park AuthorityGraduate Students(see page 34)Technical StaffLewis AndersonJames Cook UniversityMary BoyleJames Cook UniversityPaul CostelloJames Cook UniversityMaria GomezUniversity of QueenslandMizue HisanoJames Cook UniversityPaulina KaniewskaUniversity of QueenslandRichard KregeAustralian National UniversityJessica MaddamsJames Cook UniversityJames MooreJames Cook UniversityGraham MortimerAustralian National UniversityNela RosicUniversity of QueenslandMaya SrinivasanJames Cook UniversityJenn TannerJames Cook UniversityAnnameike Van Den HeuvelUniversity of QueenslandSharon WismerJames Cook UniversityBusiness TeamJennifer LappinChief Operations OfficerJames Cook UniversityDavid YellowleesAssistant DirectorJames Cook UniversityOlga BazakaFinance Manager andGraduate CoordinatorJames Cook UniversityLianne CookProject OfficerUniversity of QueenslandMonica GaffneyOffice Manager and KPI OfficerJames Cook UniversityEliza GlassonICRS Conference CoordinatorJames Cook UniversityJanet SwansonAdministrative AssistantJames Cook University2009 annual report 11

program leadersProfessor Malcolm McCullochProfessor 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 Environmentat the University of Western Australia, Perth, and a newly appointed Western Australian Premier’sFellow (2009-2013). His research interests focus on the modern part of the geologic record usingisotopic and trace element geochemical methods to determine how climate and anthropogenicprocesses have influenced both past and present marine environments with particular emphasison coral reefs. Malcolm has received a number of prestigious awards, including Fellowships of theAustralian Academy of Science (2004), the Geological Society of Australia (2007), the GeochemicalSociety (2008) and the American Geophysical Union (2002). In 2009 he was awarded the JaegerMedal in Earth Sciences by the Australian Academy of Science. Malcolm holds an HonoraryDoctorate from Curtin University, and he is an ISI Highly Cited Researcher. His 240 scientific papershave been published in leading international journals including 23 articles in Science or Nature.Professor Sean ConnollyARC Professorial Fellow Sean Connolly, from James Cook University, is Leader of Program 2:Understanding and Managing Coral Reef Biodiversity. Sean combines mathematical and statisticalmodelling with fieldwork and laboratory experiments to study the dynamics of biological turnover atall 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 theecology of rocky shores. In 1999-2000, he was a postdoctoral research fellow at the Universityof 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 modellingapplied to coral reefs. Sean has 38 publications in leading international journals, including 5 in Scienceor Nature, and he has supervised 22 Postgraduate and Honours students since 2001. He currentlyholds an Australian Professorial Fellowship from the Australian Research Council, and was mostrecently honoured by the award of the 2009 Fenner Medal of the Australian Academy of Science, forpioneering new approaches to understanding biodiversity.Professor Garry RussProfessor 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 ofreef fish of commercial and recreational fishing significance (mostly serranids, lutjanids andlethrinids). A major area of his applied research involves population and community dynamicsof reef fish of commercial significance. In the Coral Triangle region and Australia, he isundertaking long-term (25 year) monitoring of reef fish populations inside and outside marinereserves. Russ received his PhD from the University of Melbourne in 1981. Subsequentlyhe 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 Professorin Marine Biology. Garry has published over 65 papers in international journals. In 1999, hereceived a prestigious Pew Fellowship in Marine Conservation jointly with his long-timecolleague Dr. Angel Alcala. In 2007, he was awarded recognition for his contributions tomanagement of the Great Barrier Reef, by the Great Barrier Reef Marine Park Authority.12ARC Centre of Excellence for Coral Reef Studies

Professor Ove Hoegh-GuldbergProfessor Ove Hoegh-Guldberg is one of two Deputy Directors of the ARC Centre and Leader ofProgram 4: Genetic, molecular and physiological processes. He is also the Director of the newGlobal Change Institute at the University of Queensland. His research interests span a broad rangeof topics including marine biology, physiology, biochemistry and molecular biology of plant-animalsymbioses, co-evolution, coral bleaching, ocean acidification and climate change. In 1999, he wasawarded the University of NSW Eureka Prize for Scientific Research, for “research by an Australianscientist under 40”. Ove is Co-Chair of the Global Environment Facility/World Bank Working Groupon Coral Bleaching and Related Ecological Disturbances, one of three expert groups within theIntergovernmental Oceanographic Commission and World Bank Coastal Program’s Global Coral ReefTargeted Research and Capacity Building Project that includes members from the ARC Centre. Hehas published over 160 papers, including 15 in Science or Nature. He is well known as an advocatefor 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 prestigiousQueensland Premier’s Smart State Fellowship (2008-2013).Professor Terry HughesProfessor 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 HopkinsUniversity 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 electeda Fellow of the Australian Academy of Science in 2001 in recognition of “a career which hassignificantly advanced the world’s store of scientific knowledge”. He has been awarded twoFederation Fellowships by the Australian Research Council, from 2002-2012, and is a Fellow ofthe Beijer Institute for Ecological Economics, in Stockholm. In 2007 he was awarded the ShermanEureka prize for Environmental Research. He is a member of the ARC Advisory Council and BoardMember of the Resilience Alliance and the Beijer Institute. Terry has broad research interests inecology, marine biology and the social-ecological dynamics of coral reefs. As Centre Director, heprovides academic leadership and is responsible for the strategic development of the Centre. He isan ISI Highly Cited Researcher, ranked #1 in Australia for citations in Ecology & Evolution. In 2008, hewas awarded the prestigious quadrennial Darwin Medal by the International Society for Reef Studies.Professor Bob PresseyProfessor Bob Pressey was recruited by JCU in late 2007 to establish and lead the ARC Centre’snew Program 6: Conservation planning for a sustainable future. Bob’s research includes aspectsof spatial data sets on biodiversity, geographic information systems, spatial modeling of speciesand human activities, software development, explicit frameworks for deciding on the locationand timing of conservation investments, and the socio-economic issues involved in implementingconservation action. Prior to moving to JCU he was a professorial research fellow at the Universityof Queensland. Before that, he worked as a research scientist for the New South Wales NationalParks and Wildlife Service for almost 20 years. During that time, he developed and applied leadingedgetechniques in conservation planning, influenced policy and conservation practice, and begana long series of international collaborations. Along with Malcolm McCulloch and Terry Hughes he isone of three ISI Highly Cited Researchers in the ARC Centre and serves on the editorial boards of theleading conservation biology journals. Bob was awarded The Royal Botanic Gardens’ Eureka Prizefor Biodiversity Research, in 2002 and the inaugural (2008) Australian Ecology Research Award fromthe Ecological Society of Australia. His most recent recognition (2009) was the title of James CookUniversity Distinguished Professor for excellence in scholarly activities.2009 annual report 13

program leadersDr Simon FoaleSenior 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 postdoctoralfellowship 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 fisherymanagement issues in the Pacific, particularly in the Solomon Islands and Papua New Guinea. Simonhas very broad applied experience in the Pacific, having worked for non-government conservationorganisations, mining companies, regional agencies, governments and aid agencies. He publishesin a wide range of journals spanning the natural and social sciences. Simon’s current researchexamines political, social and economic aspects of fishery use and management in Melanesia, with aparticular emphasis on developing locally relevant and culturally appropriate educational resources forimproving coral reef fishery management.Professor David MillerProfessor David Miller is Leader of Program 8: Genomics and metagenomics of coral reefs. Davidstudies the molecular biology of corals and other “simple” marine animals. His research interestsspan a broad range of topics from marine biology to genomics, and include the biochemistry andmolecular 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 fromthe University of Kent (UK). He subsequently undertook post-doctoral research at the Universityof Bristol (UK) and then the University of Adelaide. David moved to James Cook University fromAdelaide in 1984 and is currently a Professor in molecular genetics and genomics. David’s main claimto fame is the discovery that “simple” animals such as corals have genomes as complex as those ofman and other vertebrates, and in highlighting the role of gene loss in shaping animal genomes. Heplays a leading role in a number of genome projects on various lower animals, including the first coralgenome project and the first all-Australian whole genome project, and is a regular commentator onanimal genome evolution for a number of high profile journals.14ARC Centre of Excellence for Coral Reef Studies

Photo by John PandolfiMedia Release7000 year old corals ofMoreton Bay tell their storyThe 7000-year-old coral communities of Moreton Bayare telling a curious tale, expanding when sea-levels riseor water quality improves, then declining when currentcirculation becomes more restricted.Intriguing new insights into the behaviour of corals andfish under changing climatic conditions will be presentedby leading marine researchers at a public forum in Brisbanethis coming Friday.Professor John Pandolfi from the University ofQueensland and ARC Centre of Excellence for CoralReef Studies and his team have been dating the corals ofMoreton Bay and finding they have undergone surges ofgrowth, probably triggered by subtle changes in sea leveland water conditions.“We’ve found coral communities up to 7000 years oldshowing these curious growth episodes – the last onestarted about 400 years ago. When coral reef growth slowsor stops in the Bay, it appears to correspond with a declinein the current circulation and an increase in turbidity.”The team has also found clear evidence of changes in thetypes of corals in the Bay from the delicate staghorns tomore massive forms, coinciding with European settlementand possibly resulting from declining water quality asnearby catchments were altered.These and many other aspects of the future of Australia’scorals will be explored at a scientific symposium andpublic forum in Brisbane this week.The scientific symposium Securing Coral Reef Futureswill take place on August 6 and 7 at the Brisbane CustomsHouse. It will be followed by the Public Forum on thefuture of the coral reefs worldwide at 6.00pm, Friday 7August at the Brisbane Convention and Exhibition Centre.Media are welcome to attend both.“Coral reef scientists and managers are worried aboutthe future, and with good reason,” Prof. Hughes says.“The world is on a conveyor belt driven by populationgrowth, rising consumption and climate change - yet mostgovernments and agencies are focused on maintaining thestatus quo, while many conservation groups would liketo return to a pristine past. In a rapidly changing world,standing still or going backwards is simply not an option.The trick is to actively steer forward to a sustainable futurethat recognizes the importance of healthy ecosystems forhuman well-being.”At the symposium eminent environmental scientistswill release an international communiqué on the future ofcoral reefs and the human communities which depend onthem under climate change. A media conference will beheld at 10.40am on Thursday, August 6, at The CustomsHouse Reid Room, where CoECRS head Professor TerryHughes, Professor John Quiggin (UQ) and Dr Josh Cinner(JCU) will be available to answer questions.Communiqué at www.coralcoe.org.au/news_stories/brisstatement.html2009 annual report 17

RESEARCHProgram 2: Understanding and Managing Coral Reef BiodiversityResearchers• Sean Connolly Program Leader• Glenn Almany Research Fellow• Andrew Baird Research Fellow•David Bellwood• Guillermo Diaz-PulidoResearch Fellow• Maria Dornelas Research Fellow• Toby Elmhirst Research Fellow• Chris Fulton• Nick Graham Research Fellow• Terry Hughes Research Fellow• Geoffrey Jones• Ronald Karlson• Philip Munday Research Fellow• John Pandolfi• Lucie Penin Visiting Research Fellow• Morgan Pratchett Research Fellow• Robert SteneckCoral reef biodiversity underpins thecritically important functions and servicesperformed by reef ecosystems, suchas sustaining the productivity of fishstocks on which many tropical nationsdepend for their food security andfuture development. Program 2 aimsto understand the mechanisms andprocesses that maintain coral reefbiodiversity, using a combination ofmathematical modelling and field studies.This multi-disciplinary approach informsknowledge-based management ofbiodiversity resulting in environmental,social, and economic benefits to tropicalmaritime nations.Program 2 research in 2009 providedseveral key breakthroughs inunderstanding how coral reefs respondto overfishing and climate change,and importantly how managementcan mediate those responses. Forexample, Phil Munday, Geoff Jonesand their graduate students publishedseveral papers in 2009 detailing theeffects of ocean acidification on coralreef fish larvae and juveniles, includingimpairment of their abilities to home inon reef habitat, and to identify and avoidpredators (see p.55). Toby Elmhirst, SeanConnolly and Terry Hughes developedmathematical models of ecosystemdynamics, which predict that the supplyof new coral juveniles to overfishedreefs from nearby protected areasdoes not enhance their resilience tocollapsing into seaweed-dominatedstates. However, spill-over of larvae canfacilitate the reversal of those collapsesback to coral-dominated states. Thisstudy highlights the importance of goodmanagement outside no-take areas forpreventing coral reef collapse, but alsoshows how no-take areas can providean insurance policy in the event thatcollapses do occur. New work by JohnPandolfi and colleagues investigatingecological baselines over centennialtime scales on the Great Barrier Reefshows convincing evidence for humaninducedshifts in species compositionassociated with European colonization.This work provides the first key evidencefor shifting baselines on the Great BarrierReef, and will aid managers in settingappropriate management goals.Program 2 researchers also madenumerous important contributions in2009 to coral reef policy issues at State,Commonwealth, and internationallevels. Future Fellow Glenn Almany isworking with The Nature Conservancyand local communities in Papua NewGuinea to establish new Marine ParkAreas for managing overfishing and theeffects of climate change. Nick Grahamis providing advice to the Great BarrierReef Foundation on the developmentof indicators of coral reef resilience.Program 2 researchers also continue tointeract with Commonwealth agenciesand other relevant parties on theproposed re-zoning of the Coral Sea.Program 2 researchers were grantednumerous awards and honours in2009. Program Leader Sean Connollyreceived the Fenner Medal from theAustralian Academy of Science; thisaward recognizes outstanding researchin biology by a scientist under the age of40. Andrew Baird was awarded an ARCFuture Fellowship, and Nick Grahamreceived an Australian PostdoctoralFellowship and a Queensland SmartFutures Fellowship. In addition, JoanaFigueredo (PhD, University of Lisbon) hasbeen awarded a postdoctoral fellowshipfrom the Portuguese Fundação para aCiência e a Tecnologia, and will be joiningProgram 2 as a Visiting Research Fellowin 2010. John Pandolfi was appointedVice-President of the Australian CoralReef Society, the world’s oldestprofessional association of coral reefscientists. Program 2 researchers, withother Centre colleagues, received ARCinfrastructure funding to establish theMarine Climate Change ExperimentalFacility at JCU, which will be used tosubstantially enhance the ARC Centre’scapacity for further study of the effect ofglobal warming and ocean acidificationon reef organisms.In addition to the award of new ARCresearch fellowships to AndrewBaird and Nick Graham, a new ChiefInvestigator, Chris Fulton from theAustralian National University, alsojoined the ARC Centre in 2009. Chrishas already forged strong links withcolleagues in Program 2, and adds anextensive record of research into theeffects of flow on organism performanceto the Centre’s portfolio of expertise.18ARC Centre of Excellence for Coral Reef Studies

Photo by Simon FoaleMedia ReleaseCorals raise hopes for survivalHope that some of the world’s corals may be able toescape destruction under climate change has emerged froma study by an international team of scientists working inFrench Polynesia in the Pacific. The researchers found thatcorals off Moorea, in the central Pacific, have rebounded onfive occasions despite sustaining heavy damage from fourbleaching events and one cyclone in the past 18 years.In particular, they were able to recover even after thereef had been swamped by weeds, says team memberDr Lucie Penin of the ARC Centre of Excellence for CoralReef Studies, James Cook University and the Universitéde Perpignan.“We conclude from this that coral reefs may notcompletely disappear as a result of climate change – assome people fear they might,” she says. (In the Earth’spast history corals have become either nearly or totallyextinct on five separate occasions, and some researcherswarn that conditions under global warming may provesimilar to those previous events.)However, Dr Penin notes that the corals studied lieon the outer reef slope of an island that is not heavilypopulated, and that the main human impact on them isfishing. “The lack of human pressure on the reef makesit more resilient,” she says. “This research suggests that,if left alone, coral reefs have the possibility to recover andre-grow.”Researcher Loïc Thibaut, James Cook University andUniversité Pierre et Marie Curie adds “One of the salientfeatures of this reef is that the fish community, and inparticular herbivorous fishes have remained at high levelsof abundance throughout the study. This might wellexplain why the coral community recovered so quicklydespite the catastrophic events it had to face.”Dr Penin said the Tiahura Outer Reef Sector of Mooreahad been closely studied for four decades by scientists,and the corals’ responses to natural disturbances werenow well understood. The five major disturbances hadreduced coral cover at the time from over 50% of the areato as little as 22% while, in the early nineties sea weedsknown as turf algae had taken over more than half of thearea in the wake of cyclone and bleaching. However keycoral species were able to re-colonise the reef in subsequentyears.“Our results support the idea that a rapid recoveryfrom a weed-dominated reef to a coral dominated oneis possible – but it will depend on what other pressuresthe corals are facing,” Dr Penin says. “It also shows that afast recovery, in just a decade, is possible under the rightconditions.”However since the study was completed the Tiahura reefhas come under a new threat – Crown of Thorns starfishhave mounted a severe attack on the corals, slashing coralcover to as little as two per cent in some areas.“We are keeping a very close eye on this outbreak. Rightnow the reef is in a very bad condition, but there are signsof recovery and we are hoping it will come back fromthis as it has from the damage caused by bleaching andcyclones,” she says.Adjeroud, M, Michonneau, F, Edmunds, P, Chancerelle, Y,de Loma, T, Penin, L, Thibaut, L, Vidal-Dupiol, J, Salvat,B and Galzin, R (2009). Recurrent disturbances, recoverytrajectories, and resilience of coral assemblages on aSouth Central Pacific reef. Coral Reefs 28(3): 775-7806 July 20092009 annual report 19

RESEARCHProgram 3: Marine Reserves and Reef ConnectivityResearchers• Garry Russ Program Leader• Glenn Almany Research Fellow• Andrew Baird Research Fellow•David Bellwood• Sean Connolly Research Fellow• Nick Graham Research Fellow• Terry Hughes Research Fellow•••••Geoffrey JonesMichael KingsfordLaurence McCookMark McCormickMark Meekan• Philip Munday Research Fellow••John PandolfiSerge Planes• Morgan Pratchett Research Fellow• David Williamson Research Fellow•Bette WillisNetworks of marine reserves (no-takeareas) are used to manage biodiversityand fisheries. Zoning for multiple levelsof use and protection, including no-takeareas, has become one of the principalmechanisms for management of marineresources in Australia and around theworld. Program 3 focuses on howmarine reserves enhance biodiversityand fisheries management. A majorissue is the level of larval dispersal andconnectivity within and between marinereserve networks. Program 3 focuses onthe optimal design of reserve networksfor coral reef conservation and fisheriesmanagement; and on the consequencesof shifts in connectivity, due to climatechange and other processes that affectstock-recruitment relationships.In 2009, Program 3 researchers,together with colleagues from Franceand the USA, published a set of sixarticles in a Special Theme section ofthe journal Coral Reefs. The papersreviewed and synthesized informationon biological connectivity on coralreefs, while also providing updatedrecommendations for the design ofmarine protected area networks (e.g.,size and spacing) to protect connectivity.These papers formed the core outputfrom an international workshop entitled“Connectivity and population resilience –sustaining coral reefs during the comingcentury” co-hosted in Townsville in2008 by the ARC Centre and GlobalEnvironment Fund.Program 3 continues to lead the worldin the development and application oftechniques for tagging and trackingmarine larvae. Geoff Jones andcolleagues used larval tagging andgenetic studies to reveal the export oflarvae from marine reserves in PapuaNew Guinea. They showed that larvaldispersal connected fish populations in anetwork of marine protected areas overscales of 30km. This ground-breakingresearch was published in 2009 inProceedings of the National Academy ofScience. This year, for the first time, wealso applied these novel larval trackingtechniques, combined with detailed larvaldispersal modeling, to Australia’s iconicGreat Barrier Reef Marine Park.Program 3 continues to makebreakthroughs in understanding of larvalbiology. Mark McCormick and colleaguescompleted a synthesis of how thephysiological state of parents (particularlymothers) during gametogenesisaffects offspring success. This novelresearch shows that successfulrecruitment to the next generation ofbreeding fish is strongly influencedby parental condition. Phil Mundayand colleagues showed that oceanacidification impairs the innate abilityof fish larvae to avoid their predators.If acidification continues unabated,the impairment of sensory ability willreduce population sustainability of manymarine fish species, with potentiallyprofound consequences for marinebiodiversity, fisheries sustainability andconnectivity patterns of populationsand networks of marine reserves.In the Philippines, Garry Russ andcolleagues undertook a national-scaleassessment of the current extent,conservation efficacy and gaps incoverage of Marine Protected Areas(MPAs), using a newly compiled GISdatabase with records for more than1000 marine reserves. The analysisshows that the current extent anddistribution of MPAs does not adequatelyrepresent biodiversity in the Philippines.At present, only 2.8% of coral reef areain the Philippines is protected withinno-take zones, and 88% of MPAs aresmaller than 1km 2 . However, spacingdistances between MPAs are suchthat larval connectivity between sitesis likely, providing opportunities todevelop regional-scale MPA networks.The results indicate that, even ifadopted universally, community-basedMPAs will not be sufficient to meetnational goals. A dual approach to MPAimplementation was recommended,whereby continued efforts to increasethe number of community-based MPAsare supplemented by the designationof additional large no-take areas with aconservation focus.Many of the research projects withinProgram 3 are designed to activelyengage with local stakeholders. Forexample, work on the Great BarrierReef in 2009 required assistance fromseveral recreational fishing groups,including the major recreational fishingbody in Queensland, SUNFISH. In thePhilippines, Garry Russ’s long-standingcolleague, Angel Alcala, continues towork closely with Philippine fishingcommunities to set up marine reserves.In PNG and the Solomon Islands, FutureFellow Glenn Almany and others workclosely with The Nature Conservancy totest and design new Marine ProtectedArea networks.Research on the design andimplementation of marine reservenetworks, as outlined above for theGreat Barrier Reef, Papua New Guinea,the Solomon Islands and the Philippines,represents a significant contribution byProgram 3 to the scientific knowledgeunderpinning the Coral Triangle Initiative(see also p.26, 28, 50).20ARC Centre of Excellence for Coral Reef Studies

Photo by Ashley FrischMedia ReleaseProof that marine parks workNew evidence supports the growing view that a networkof marine reserves is more effective for maintaining adiversity of fish and other marine species than a single,isolated park or no-fishing area.An international research team has found that networksof marine protected areas (MPAs) can play a big role inprotecting threatened coral reef fish and other marinespecies from local extinction. In a world-first experiment,the researchers used DNA fingerprinting to show thatbaby orange clownfish have remarkable homing abilities,with many finding their way back to home reefs afterbeing swept out to sea as hatchlings.In the process they discovered some baby clownfish hadtravelled to reefs as much as 35 kilometres distant fromthe reef where they were spawned – a spectacular featconsidering they were only a few millimetres in length.The research was carried out in Kimbe Bay, New Britainin Papua New Guinea, a region of relatively pristine coralreefs where it is proposed to set up a network of marinereserves.“Using their parent’s DNA to identify where they hadcome from, we have been able to show that about 40 percent of baby clownfish that settle in a marine reserve arethose that have returned home. In addition, the parentswithin one marine reserve can explain up to 10 per centof the baby fish settling in reserves 20-30km away”, saysProf Geoff Jones of the ARC Centre of Excellence for CoralReef Studies.“This shows not only how effective a marine protectedarea can be for conserving the breeding stock on aparticular reef – but also how important it is to have anetwork of protected reefs at the right distance which canhelp to re-stock one another.”In another first, the team has demonstrated the powerof parental DNA analysis for measuring the health andviability of fish populations in marine protected areas.Because orange clownfish live in sea anemones andbecause the locations of all the anemone clumps aroundKimbe Island were known, the team was able to collectDNA from 506 adult clownfish living around the island –which they believe to be its entire population.They then tested juvenile fish which had recentlyreturned from the open sea and settled on the reef in orderto establish their parentage, finding that about 40 per centwere locally-bred while the remainder had come fromother reefs.“This level of recruitment to the home reef wasremarkably stable over time. It shows both the valueof having a protected area to maintain the local fishpopulation – and also the importance of having a networkof protected areas within a range that allows them toreplenish one another’s fish populations,” Professor Jonessays.“Given the mounting evidence worldwide thatpopulations of many small reef fish are under threat, wethink parental DNA analysis offers a new tool to helpprotect them.”Planes, S, Jones, GP and Thorrold, SR (2009). Larvaldispersal connects fish populations in a network ofmarine protected areas. Proceedings of the NationalAcademy of Sciences 106(14): 5693-5697.25 March 20092009 annual report 21

RESEARCHProgram 4: Genetic, Molecular and Physiological ProcessesResearchers• Ove Hoegh-GuldbergProgram Leader• Tracy Ainsworth Research Fellow• Ken Anthony• Line Bay Research Fellow• Guillermo Diaz-PulidoResearch Fellow• Sophie Dove• Simon Dunn Research Fellow• Bill Leggat• David Miller• Madeleine van Oppen• Bette Willis• David YellowleesProgram 4 researchers continued in 2009to investigate the relationships betweenthe coral animal and their symbioticmicroalgae, and microbial associates –both as beneficial partners and diseaseagents. A major focus within the Programhas been determining the impactthat environmental factors – includingglobal climate change – have on theserelationships, and particularly on an arrayof projects that address the mechanismsof coral bleaching triggered by thermalstress. These studies greatly increaseour knowledge of these symbioses,providing a broader understanding ofhow and why corals respond in certainways to different stressors.Eugenia Sampayo in the Hoegh-Guldbergand Dove laboratories have analysedeight ecologically distinct Symbiodiniumspp and showed that there was a strongcorrelation between phylogeneticallyindependent lineages and ecologicaland physiological attributes. The Willisand van Oppen laboratories, in studyingthe relationship between the coralhost and zooxanthellae, have nowshown that it can take up to 3 yearsto establish adult patterns of algalendosymbioses. This is a remarkablefinding, with important implications forhow reefs recover from recurrent boutsof bleaching. Along with the work ofPhD students David Abrego and JosMieog, these studies have revealedfresh insights into the complexity ofthe symbiosis between these partners.Interestingly, they have shown moreclearly than any previous studiesthat the fitness of this relationship isinfluenced by interactions between thesymbiont type and the environment.The impact of climate change on thesymbiotic association is a major focusof all researchers in Program 4, acrossboth the UQ and JCU/AIMS nodes,with a wide range of important researchquestions being addressed. PhD studentRachael Middlebrook demonstrated thatheating rate is an important parameterwhen determining thermal susceptibilityof corals. The shuffling or switching ofsymbionts (the “adaptive bleaching”hypothesis) came under scrutiny whenPhD student Michael Stat and coworkersfound no evidence for switchingin ten coral species 12 months after athermal stress event on the Great BarrierReef. Gene expression studies, led byQueensland Smart State Fellow LineBay, have revealed evidence of majorphenotypic plasticity in gene expressionlevels in response to environmentalchange. Line and co-workers’ ongoingstudies are exploring the genetic basisof trait variation, to assess the potentialfor adaptation by corals in response toclimate change and to potentially findgenetic markers associated with thetolerance of corals to climate change.Also of relevance to global warming wasthe 2009 study by Mia Hoogenboomwhich showed that, contrary toconventional thinking, the optimal lightregimes for coral growth and energeticsare below the maximum observed lightlevels of coral reefs.Simon Dunn, Sophie Dove, Bill Leggatand Tracy Ainsworth have been exploringthe involvement of cell death pathwaysin thermal stress and breakdown ofthe symbiosis between corals andtheir dinoflagellates. This has led to theidentification of a series of key genesthat control the fate of cells affected byrapid changes in sea temperature.Research into causative agents of coraldiseases by Program 4 researchers isadding to the toolbox available to reefmanagers. A study by PhD student YuiSato is the first to describe the seasonaldynamics of an outbreak of black banddisease on the Great Barrier Reef, whichhighlights the increasing susceptibilityof corals to rising sea temperatures.Early successional changes in bacterialcommunities that facilitate developmentof black band disease were identified andwill aid in early detection of the disease.A complementary study of the naturalbacterial communities in corals, by TracyAinsworth showed that they too aresignificantly altered during thermal stress.Landmark studies by PhD student MeirSussman identified Vibrio coralliilyticus asa causative agent of white syndromes,a group of damaging Indo-Pacificcoral diseases, and showed thatphotoinactivation of algal endosymbiontsby zinc-metalloproteases contributesto its virulence. These studies lay thegroundwork for developing assays thatwill provide important management toolsfor detecting future disease outbreaks.22ARC Centre of Excellence for Coral Reef Studies

Photo by Ove Hoegh-GuldbergMedia ReleaseReef boom beats doomMarine scientists say they are astonished at thespectacular recovery of certain coral reefs in Australia’sGreat Barrier Reef Marine Park from a devastating coralbleaching event in 2006.That year high sea temperatures caused massiveand severe coral bleaching in the Keppel Islands, in thesouthern part of the Great Barrier Reef. The damaged reefswere quickly smothered by a single species of seaweed –an event that can spell the total loss of the corals.However, a lucky combination of rare circumstancesmeant the reefs were able to achieve a spectacular recovery,with abundant corals re-established in a single year. DrGuillermo Diaz-Pulido explains that “Three factors werecritical. The first was exceptionally high re-growth offragments of surviving coral tissue. The second was anunusual seasonal dieback in the seaweeds, and the thirdwas the presence of a highly competitive coral species,which was able to outgrow the seaweed.”“It is rare to see reports of reefs that bounce back frommass coral bleaching or other human impacts in less thana decade or two,” said Dr Diaz-Pulido. “But this also allhappened in the context of a well-protected marine areaand moderately good water quality,” he adds.“The exceptional aspect was that corals recovered byrapidly regrowing from surviving tissue. Recovery ofcorals is usually thought to depend on sexual reproductionand the settlement and growth of new corals arriving fromother reefs. This study demonstrates that for fast-growingcoral species asexual reproduction is a vital component ofreef resilience” says Dr Sophie Dove.“Coral reefs globally are increasingly being damagedby mass bleaching and climate change, and their capacityfor recovery from that damage is critical to their future,”explains Prof. Ove Hoegh-Guldberg. “Our study suggeststhat managing local stresses that affect reefs such asoverfishing and declining water quality can have a biginfluence on the trajectory of reefs under rapid globalchange.”“Clearly, we need to urgently deal with the problem ofrising carbon dioxide in the atmosphere, but managingreefs to reduce the impact of local factors can buy importanttime while we do this,” he says.Understanding the different mechanisms of resilienceis critical for reef management under climate change.“Diversity in processes may well be critical to the overallresilience and persistence of coral reef ecosystems globally,”Dr Laurence McCook, from the Great Barrier Reef MarinePark Authority, says.“This combination of circumstances provided a luckyescape for the coral reefs in Keppel Islands, but is alsoa clear warning for the Great Barrier Reef. As climatechange and other human impacts intensify, we need todo everything we possibly can to protect the resilience ofcoral reefs,” he adds.Diaz-Pulido, G, McCook, LJ, Dove, S, Berkelmans, R, Roff,G, Kline, DI, Weeks, S, Evans, RD, Williamson, DHand Hoegh-Guldberg, O (2009). Doom and boom ona resilient reef: climate change, algal overgrowth andcoral recovery. PLoS ONE 4(4): e523922 April 20092009 annual report 23

RESEARCHProgram 5: Resilience of Linked Social-Ecological SystemsResearchers• Terry Hughes Program Leader• Andrew Baird Research Fellow•David Bellwood• Joshua Cinner Research Fellow• Toby Elmhirst Research Fellow• Kathryn Ferguson Research Fellow• Pedro Fidelman Research Fellow• Simon Foale Research Fellow•Carl Folke• Nick Graham Research Fellow••Laurence McCookJohn Pandolfi• Bob Pressey Research Fellow• Robert SteneckProgram 5 focuses on the interfacebetween people, economies and coralreef ecosystems. Our objective is toundertake research and develop newtools that improve the governanceand management of natural systemsand enhance their capacity to sustainhuman and natural capital. Program5’s multi-disciplinary researchcombines expertise on coral reefbiology, management, governance,economics and the social sciences.In February, Program 5 leader TerryHughes and Rodrigo Bustamante fromCSIRO, co-hosted the latest of theARC Centre’s series of internationalworking group meetings on marinesocial-ecological systems, focussingthis time on the Galapagos Islands. Thegroup examined how climate change,tourism, global markets, migration, andintroduced pests have all changed thenature and scale of the social-ecologicaldynamics of the Galapagos archipelago,with the co-evolution of an emergingsystem of governance. The next meetingwill be held in June 2010 in the BalticSea, addressing the challenges of transboundarygovernance in the ocean.In June, Terry Hughes joined theinaugural Science Committee responsiblefor developing a 10-year global researchproject of ICSU, the InternationalCouncil for Science. The project, entitledProgram on Ecosystem Change andSociety (PECS), will focus on bothhuman development and sustainabilityof natural resources at regional to globalscales. PECS aims to link science andenvironmental management to society,policy and human well-being. The PECSScience Committee will meet twice ayear in Paris to develop a social-ecologicalresearch agenda that is closely alignedto the ARC Centre’s Programs 5, 6 and7. PECS is co-sponsored by UNESCO,and will complement existing globalenvironmental change programs andinternational partnerships.Two of the ARC’s high-profile articles in2009, published in Science and Nature,are at the interface of Programs 5 and 7.The first argues that coping with globalchanges requires new institutions anda global system of governance that iscurrently missing. Energy, food andwater crises, climate change, decliningworld fisheries, emerging diseases andantibiotic resistance are all examplesof intertwined global challenges thatare outpacing the capacity of existinginstitutions (see p.29). The Nature paperproposes ten earth-system boundarieswhich should not be exceeded to avoidcrossing dangerous tipping points. Theseinclude the rate of species extinction,the amount of nitrogen and phosphorusin fertilisers, use of fresh water, theclearing of land, ozone depletion, aerosolpollution of the atmosphere and chemicalcontamination. These two studiesreflect the ARC Centre’s ongoing linksto the Resilience Alliance, the BeijerInstitute for Ecological Economics,and the Stockholm Resilience Centre.Other major publications during the yearincluded a cutting-edge theme sectionin the journal Coral Reefs, on larvalconnectivity and ecological resilience(see Program 3 summary), compiled andedited by Geoff Jones, Garry Russ, PeterSale and Bob Steneck.Senior Fellow Simon Foale wascontracted by The Nature Conservancy(TNC) to review the extent to whichTNC have applied the ecosystemapproach to fisheries in their Melanesianprojects. ARC Australian PostdoctoralFellow Josh Cinner and colleaguesundertook a regional analysis of therole of socioeconomic developmentin sustaining coral reefs in the IndianOcean. The study, published in CurrentBiology, was also presented by Joshat the 2009 meeting of the AmericanAssociation for the Advancement ofScience, in Chicago. Research FellowToby Elmhirst and colleagues presentedthe results of a novel modelling studyin the December issue of Coral Reefs,which examines the reliance of highlyprotectedareas on larval input from thesurrounding seascape. Most research inlarge scale connectivity has emphasizedspill-over from no-take areas. Toby’s workpredicts that the ecological resilienceof no-take areas can be undermined bydegradation at larger scales, requiring aseascape approach to marine resourcemanagement beyond the conventionalfocus on networks of no-take areas.24ARC Centre of Excellence for Coral Reef Studies

Photo by Simon FoaleMedia ReleaseGear bans “can help save reefs”An international team of scientists led by Dr Josh Cinnerof the ARC Centre of Excellence for Coral Reef Studies hasproposed that bans on fishing gear - like spear guns, fishtraps, beach seine nets, and gill nets – could aid in therecovery of reefs and fish populations hard hit by coralbleaching events.Research carried out in Kenya and Papua New Guineahas shown that certain types of gear are more damagingto corals, to coral-dependent fish and to the key species offish that are needed to help reefs recover from bleachingor storm damage.“This is creating a double jeopardy for both the coralsand certain types of reef fish. They are already on the edgebecause of the overfishing – and the additional impactcaused by a bleaching event can push them over” DrCinner explains. The result can be an accelerated declineof the reef, its fish populations and their ability to sustainlocal people.“From an ecological perspective, the best response tobleaching is to close reefs to fishing entirely. But that is notfeasible everywhere and is a particularly hard sell amongthe impoverished fishers in developing countries” says coauthorDr. Tim McClanahan of the Wildlife ConservationSociety. “In areas where fishery closures are impractical,managers don’t have many options and haven’t been ableto do much but watch the reef die and often not recover.”The team investigated the effects of five main types ofgear on different types of fish: spear guns, traps, hook andline, beach seine nets and gill nets.“Spear guns target a high proportion of species that helpmaintain the resilience of coral reefs, but also can result ina surprising amount of damage to the corals themselves.When a fish is shot with a spear gun, it often hides in thereef, so some fishermen break the corals in their attemptsto get it.” Dr Cinner says.But in developing countries, spear guns can be thefishing tool most used by the poorest fishers because theyare cheap to make and the yield can be high, so they are animportant source of income for poor fishers.“You can’t simply impose an arbitrary ban on theiruse – you need to consider issues like compensation,other fishing options, or alternative livelihoods for theaffected fishers,” says co-author Dr. Shaun Wilson of theWestern Australian Department of Environment andConservation. “One key issue may be educating fishersabout the importance of reef habitat and the species thathelp to maintain reef quality – and the need to be selectivein what they shoot. This would mean fishers could still usethis cheap and effective fishing tool without necessarilydamaging habitat and reef resilience.”Cinner, JE, McClanahan, TR, Graham, NAJ, Pratchett, MS,Wilson, SK and Raina, J-B (2009). Gear-based fisheriesmanagement as a potential adaptive response to climatechange and coral mortality. Journal of Applied Ecology 46:724-73218 June 20092009 annual report 25

RESEARCHProgram 6: Conservation Planning for a Sustainable FutureResearchers• Bob Pressey Program Leader• Glenn Almany Research Fellow• Natalie Ban Research Fellow•Debora de Freitas• Tatjana GoodVisiting Research Fellow• Johnathan Kool Research Fellow• Laurence McCookProgram 6, established in 2008,focuses on spatial solutions to resourcemanagement problems, involving thedesign of conservation areas that aremanaged to promote the persistenceand sustainable use of natural resources,and implemented with local communitiesand other stakeholders. During 2009 ournumber of PhD students grew to nineand further growth is planned for 2010,with the recruitment of two additionalResearch Fellows.The Great Barrier Reef and the CoralTriangle region are both a major focusof Program 6, and Bob Pressey andcolleagues have already built closelinks with local governments, stategovernments, Australian governmentdepartments, Natural ResourceManagement (NRM) boards, internationalconservation NGOs, International Unionfor Conservation of Nature (IUCN - theWorld Conservation Union) and theUnited Nations Environment Program.During 2009, Pressey established newcollaborative links with two NRM Boardsin north Queensland. With Allan Dale,CEO of Terrain (Wet Tropics), the NRMBoards, and Debora de Freitas, Presseyis designing a research project to providemanagers of coastal catchments withthe tools to make effective trade-offsbetween the many objectives they haveto balance. A keynote presentation byPressey at the inaugural Island Arkssymposium led to a major fundingapplication to the Federal government incollaboration with Derek Ball, OperationsManager of Reef Catchments (MackayWhitsundays) NRM.Natalie Ban and Bob Pressey contributedto two working groups of the GreatBarrier Reef Foundation to discuss theimportance of dynamics such as coralbleaching and pelagic productivity forplanning multiple-use reef zones. Thisinvolvement led to Natalie’s successfulapplication for the Foundation’s inauguralBommies Award, shared with EddieGame of The Nature Conservancy.They will use the award funding tohold a scientific workshop on howto incorporate patch dynamics intoconservation planning for the GreatBarrier Reef region. Research Fellow,Johnathan Kool, who is co-funded by theAustralian Institute of Marine Science(AIMS), has begun work on the extensiveCSIRO-AIMS seabed biodiversity data setfor the Great Barrier Reef. He is analysingthese data to help inform marineclassification and conservation objectives.Program 6 has launched a number ofnew projects in the Coral Triangle andthe south-west Pacific. For instance,in 2009 Johnathan Kool completed aunique model of ocean circulation inthe Coral Triangle region. Johnathanalso leads a new project in the SolomonIslands, in collaboration with The NatureConservancy, identifying marine andterrestrial bioregions as a basis for agap analysis of protected areas andidentification of preliminary additionalprotected areas that link catchments andinshore waters. In Fiji, Program 6 hasinitiated a project with one of our formerpostdoctoral fellows, Stacy Jupiter ofthe Wildlife Conservation Society, toestimate the opportunity costs to localcommunities of establishing marineprotected areas in inshore waters.In Papua New Guinea, Natalie Banhas developed her research projecton patch dynamics and conservationplanning within the Bismarck Sea andthe Great Barrier Reef. Natalie also leda consultancy for the Pew Foundationto estimate the management costs ofcomplete no-take and partial no-takescenarios for the proposed Coral SeaMarine Reserve.The Program had a busy and productive2009. As well as her award from theGreat Barrier Reef Foundation, Nataliereceived an Australian PostdoctoralFellowship from the ARC. Bob Presseyand Helene Marsh were awarded anARC Linkage grant entitled “Innovativesystematic conservation planning forindigenous land and sea country: TorresStrait as a case study”. The grant willfund a new Research Fellow for threeyears to combine Indigenous knowledgewith software tools for participatoryplanning of harvesting restrictions inTorres Strait.Program 6 researchers and PhDstudents attended national conferencesin Alice Springs, Brisbane, Canberra,Newcastle and the WhitsundayIslands and international conferencesin China, the Czech Republic, Fiji,Indonesia (two meetings), Portugal,Tahiti, and the USA (two meetings).Attendance at these conferencesinvolved a total of 36 presentations,including three invited keynotes.26ARC Centre of Excellence for Coral Reef Studies

The Great Barrier Reef as seen from spaceMODIS satellite image (http://visibleearth.nasa.gov)Photo courtesy NASAMedia ReleaseRules proposed to save the world’s coral reefsAn international team of scientists has proposed a set ofbasic rules to help save the world’s imperiled coral reefsfrom ultimate destruction.Their proposal is being unveiled at the World OceanConference 2009 in Manado, Indonesia, where leaders ofsix regional governments plus Australia and the UnitedStates are meeting to declare the largest-ever marinereserve in world history, the Coral Triangle Initiative.“The catastrophic decline in the world’s coral reefsdemands urgent management responses on two fronts,”say the researchers from the ARC Centre of Excellencefor Coral Reef Studies, The Australian Museum, WoodsHole Oceanographic Institution, James Cook University,University of Perpignan, the United Nations Universityand The Nature Conservancy.These are the “...reduction of immediate direct threatssuch as climate change, over-fishing and water pollution,and actions to protect or enhance the resilience of reefecosystems in the face of existing and unavoidable futurethreats,” they say.The key to saving threatened coral ecosystems is tomaintain the links (connectivity) between reefs allowinglarvae to flow between them and re-stock depleted areas,the team led by Pew Fellow Dr Laurence McCook ofAustralia’s Great Barrier Reef Marine Park Authorityargues.The researchers propose six ‘rules of thumb’ for keepingcoral ecosystems viable, based on the results of researchcarried out in the Philippines, Australia, and Papua NewGuinea.These rules are:1. allow margins of error in extent and nature ofprotection, as insurance against unforeseen threats;2. spread risks among areas;3. aim to create networks of protected areas which (a)protect all the main types of reef creatures, processesand connections, known and unknown; (b) achievesufficient protection for each type of reef habitattype, and for the whole region; (c) achieve maximumprotection for all reef processes (d) contain severalexamples of particular reef types to spread the risk;4. protect whole reefs where possible; place bufferzones around core areas;5. allow for reef species to spread over a range ofdistances, especially 20–30 km; and6. use a range of conservation approaches, includingmarine protected areas.The rules are designed to operate in a range of situations,including where detailed scientific knowledge of localcoral reefs and their species is sparse, the team says in areview article in the journal Coral Reefs.“The Coral Triangle Initiative is one of the most importantmarine conservation measures ever undertaken anywherein the world and the first to span several countries. Itinvolves Indonesia, the Philippines, Malaysia, PapuaNew Guinea, East Timor and the Solomon islands, andis as much about nation building and food security as itis about reef conservation” says Professor Terry Hughes,Director of the CoECRS, attending the Coral Trianglemeeting today in Manado, Indonesia.McCook, L, Almany, G, Berumen, M, Day, J, Green, A,Jones, G, Leis, J, Planes, S, Russ, G, Sale, P and Thorrold,S (2009). Management under uncertainty: Guide-linesfor incorporating connectivity into the protection ofcoral reefs. Coral Reefs 28(2): 353-366.11 May 20092009 annual report 27

RESEARCHProgram 7: Policy Development, Institutions and Governance of Coral ReefsResearchers• Simon Foale Program Leader• Joshua Cinner Research Fellow• Pedro Fidelman Research Fellow•John Pandolfi• Terry Hughes Research FellowProgram 7, launched in 2009 and led bySenior Research Fellow Simon Foale,addresses the multi-faceted challengesof improving coral reef governance.Because it is people, rather than fish orcoral that must be managed, this multidisciplinaryresearch program coverscultural, political, historical, and economicaspects of coral reef management atmultiple scales. While Program 7’sactivities include a focus on the GreatBarrier Reef, they are global in scope(see press release). In 2009, most ofthe Program’s projects were directedat the rapidly evolving coastal resourcemanagement and governance challengesin the Indo-Pacific region, in particularin Melanesia and the Coral Triangle.Program 7 addresses the global politicaland economic drivers of resource-use atseveral scales, and aims to understandthe cultural, social and politicaldimensions of coral reef tenure systemsand resource use, both contemporaryand historical. Program 7 is alreadyinvolved in capacity-building activities inmany countries, working with NGOs andnational governments.This new program is rapidly rampingup with the recruitment late in 2009of two additional post-doctoral fellowsLouisa Evans and Mike Fabinyi, who willcommence in May 2010. Louisa’s Ph.D.at the University of East Anglia focussedon governance and marine systems inKenya and she is currently a researchfellow at WorldFish in Malaysia. Mikeis an anthropologist currently at theAustralian National University workingon social equity and marine resourceregulation in the Philippines. Thesetwo new recruits will provide a greatergeographic spread of expertise andprojects in Program 7.Other research fellows with a role inProgram 7 include Josh Cinner andPedro Fidelman. In 2009 Josh held aworkshop on fisheries co-managementin La Reunion, gave a keynote talk ongovernance at the Western Indian OceanMarine Science Association (WIOMSA)Conference, participated in a WIOMSAresearch priority-setting round tableon climate change and gave talks at anumber of research institutions in theUSA with governance or policy-relatedthemes. Pedro presented a paper at theEarth System Governance Project (partof the International Human DimensionsProgramme on Global EnvironmentalChange) on the institutional dimensionsof environmental governance, andwas admitted as a fellow of theEarth Systems Governance Project.He also commenced collaborationswith the Stockholm ResilienceCentre on research into governanceof large marine ecosystems, andwith CSIRO and the University ofGeorgia, USA on the institutionaldimensions of climate change.In the Solomon Islands and PapuaNew Guinea, Program 7 is undertakingsocial and ecological research onhow to develop locally relevant andculturally appropriate educationalresources for improving coral reef fisherymanagement. During the latter half of2009, Simon consolidated a productiveworking relationship with key personnelin the Curriculum Development Centre ofthe Department of Education in SolomonIslands. This work with EducationDepartments on high school sciencecurricula addresses the need for trainingin the biology and ecology of over-fishingand reef ecosystem degradation and isessential for the future leaders of thecommunity. Other aspects of this threeyear research project address the social,political and economic aspects of coralreef fishery governance at various levels.In July and August the Centre completeda long-term consultancy with theAusAID-funded Community SectorProgram in Solomon Islands – a programled by Simon Foale, which has providedvaluable research material on communitybasedsustainable development andcapacity building. In October, Simon andcolleagues at the Australian Institute ofMarine Science organised a workshopaddressing the challenge of developingsustainable livelihoods in the Indo-Pacificregion as part of the Global EnvironmentFacility’s International Waters conferencein Cairns.In 2010, Program 7 researchers will hostthree working groups, on sustainableartisanal fisheries (led by Simon Foalein collaboration with WorldFish, inTownsville), trans-boundary governancein the sea (Terry Hughes, in Stockholm),and on legal frameworks for incorporatingecological knowledge (John Pandolfi, inWashington DC).28ARC Centre of Excellence for Coral Reef Studies

Photo by Simon FoaleMedia ReleaseMissing institutions for dealingwith global crisesThe world faces a compounding series of crises drivenby human activity, which existing governments andinstitutions are increasingly powerless to cope with, agroup of eminent environmental scientists and economistshas warned. In today’s issue of the leading internationaljournal Science, the researchers say that nations alone areunable to resolve the sorts of planet-wide challenges nowarising.Pointing to global action on ozone depletion (theMontreal Protocol), high seas fisheries and antibioticdrug resistance as examples, they call for a new order ofcooperative international institutions capable of dealingwith issues like climate change – and enforcing compliancewhere necessary.“Energy, food and water crises, climate disruption,declining fisheries, ocean acidification, emerging diseasesand increasing antibiotic resistance are examples of serious,intertwined global-scale challenges spawned by theaccelerating scale of human activity,” say the researchers,who come from Australia, Sweden, the United States,India, Greece and The Netherlands.“These issues are outpacing the development ofinstitutions to deal with them and their many interactiveeffects. The core of the problem is inducing cooperation insituations where individuals and nations will collectivelygain if all cooperate, but each faces the temptation to freerideon the cooperation of others.”“There are few institutional structures to achieve cooperationglobally on the sort of scales now essential toavoid very serious consequences”, warns lead author DrBrian Walker of Australia’s CSIRO.While there are signs of emerging global action on issuessuch as climate change, there is widespread inaction onothers, such as the destruction of the world’s forests togrow biofuels or the emergence of pandemic flu throughlack of appropriate animal husbandry protocols.“Knowing what to do is not enough,” says Dr Walker.“Institutional reforms are needed to bring about changesin human behaviour, to increase local appreciation ofshared global concerns and to correct the sort of failures ofcollective action that cause global-scale problems.”“We are not advocating that countries give up theirsovereignty,” adds co-author Professor Terry Hughes,Director of the ARC Centre of Excellence for Coral ReefStudies. “We are instead proposing a much stronger focuson regional and worldwide cooperation, helped by betterdesignedmulti-national institutions. The threat of climatechange to coral reefs, for example, has to be tackled ata global scale. Local and national efforts are alreadyfailing.”“The major powers must be willing to enforce anagreement – but legitimacy will depend on acceptance bynumerous and diverse countries, and non-governmentalactors such as civil society and business,” they add.“To address common threats and harness commonopportunities, we need greater interaction amongstexisting institutions, and new institutions, to help constructand maintain a global-scale social contract,” the scientistsconclude.Walker, B, Barrett, S, Polasky, S, Galaz, V, Folke, C,Engstrom, G, Ackerman, F, Arrow, K, Carpenter, S,Chopra, K, Daily, G, Ehrlich, P, Hughes, T, Kautsky, N,Levin, S, Maler, K-G, Shogren, J, Vincent, J, Xepapadeas,T and de Zeeuw, A (2009). Looming global-scale failuresand missing institutions. Science 325(5946): 1345-134611 September 20092009 annual report 29

RESEARCHProgram 8: Genomics and Metagenomics of Coral ReefsResearchers• David Miller Program Leader• Tracy Ainsworth Research Fellow• Line Bay Research Fellow• Simon Dunn Research Fellow• Sylvain Forêt Research Fellow• Lauretta Grasso Research Fellow••• • Ove Hoegh-GuldbergBill LeggatAurélie MoyaVisiting Research FellowMadeleine van OppenThe establishment of Program 8 in 2009recognises the growing importanceof genomics in coral reef researchand the Centre’s growing expertiseand leadership in this field. The newresearch program is based aroundthe structure and function of thegenomes of corals, their dinoflagellatesymbionts and associated bacterialand viral communities, known asthe ”holobiome”. The long-term aimof Program 8, in association withProgram 4, is to understand howthe “holobiome” functions undernormal and stressed conditions.The major research highlight of 2009was the selection of the coral Acroporamillepora as the first animal to undergowhole genome sequencing andassembly by an all-Australian team. Rapidadvances in sequencing technology andthe new ground-breaking partnershipbetween the ARC Centre, The AustralianGenome Research Facility and IlluminaInc, (see opposite) has made this projectpossible. A key factor in the decisionwas the extensive transcriptome dataaccumulated by David Miller at JamesCook University and his collaborators atthe Australian National University. Thesedata have proven to be an invaluableresource, making Acropora milleporathe coral of choice for molecular and cellbiology research by most scientists in thecoral research community.In Program 8’s first year, David Miller andhis group have made significant progresswith a novel, comprehensive analysis ofthe coral transcriptome. This project hasbeen assisted by the recruitment of DrSylvain Forêt, a bioinformatician and thefirst postdoctoral fellow in the Program,co-funded by the Australian Institute ofMarine Science. Sylvain collaboratedpreviously with the Miller group on thecoral transcriptome project while on thestaff at ANU and is now a key participantin the A. millepora genome assemblyteam. The first iteration of the genomeassembly has been completed and theteam members are looking forward tothe second run which will be available inthe second quarter of 2010.Program 8 researchers are alsoengaged in unravelling the uniquenature of the transcriptome of thecoral’s photosynthetic dinoflagellatesymbionts. In addition to obtaininga more comprehensive coverageof the transcriptome, they haveprovided an interesting insight into theevolution of these organisms throughcharacterisation of the light-harvestinggene complement of the dinoflagellatesymbionts. The research of PhDstudent, Lynda Boldt, in Bill Leggat’sgroup has shown this to be the mostcomplex repertoire of such proteinsidentified in any organism to date.Research on the virome was greatlyassisted by the visit of Rebecca Vega-Thurber (Florida International University)and two of her group from the US duringthe 2009 coral spawning period on theGreat Barrier Reef. This collaborationenabled the collection of material forcharacterisation of the viral componentassociated with the coral Acroporamillepora. The analyses of the virome,along with screening the coral genomefor genes of viral origin, is underway.Other research highlights in 2009included major advances towards theestablishment of stable cell lines fromcoral (Alejandro Reyes-Bermudez) andthe identification of more members ofa unique group of genes that encodekey components of the organic matrixof corals (Reyes-Bermudez & Zhiyi Lin).David Miller analysed the homeoboxgene repertoire in the genome ofSchistosoma japonicum, while SylvainForêt was a member of the team thatanalysed the genomes of three Nasoniaspecies. Both resulted in authorship ofNature papers.PhD student Marcelo Kitahara wasan invited participant at the FAOworkshop on the identification ofdeep-sea species, held in Rome inDecember. He subsequently preparedthe Global List of Cold Water Coralsto be used as the basis for a series ofidentification guides that will be theglobal reference on the subject. Marcelowas also an invited participant at a5-day workshop entitled Systematicsand evolution of scleractinian coralsat the National Museum of NaturalHistory of the Smithsonian Institutionin Washington DC, held in June. Theworkshop was sponsored and fundedby the Encyclopaedia of Life (EOL), withadditional support from the Treatise onInvertebrate Palaeontology (TIP).30ARC Centre of Excellence for Coral Reef Studies

CentArticlerein Discovery sNewsletter: Spring 2009 reproducedwith thanks to the Australian Research CouncilCENTRES OF EXCELLENCEAustralia’s first fullgenome projectgets green light• One of the corals that form the backbone of theGreat Barrier Reef will be the first animal to have itsgenes fully explored in Australia.The program to sequence the entire genome, or geneticinformation, of Acropora millepora—a branching coralwhose ‘staghorn’ shape and beautiful colours are familiarto millions of visitors to the Great Barrier Reef—marks amajor milestone in Australian biotechnology: it will be thefirst animal genome to be fully sequenced and assembledin Australia.The staghorn coral may look like a simple animal, but itsgenome is surprisingly large and complex. In fact, Acroporamillepora has around 20 000 genes—about the same numberas a human. Why such apparently simple animals as coralsshould require as many genes as humans is still unclear; but itwas this coral which provided the first hints of how geneticallycomplex simple animals can be.While they don’t much resemble humans, corals lie deepon the ancestral tree of all animals and share many of ourgenes, says Professor David Miller, head of the GenomicsProgram at the Australian Research Council (ARC) Centreof Excellence for Coral Reef Studies, based at JamesCook University.“Acropora millepora is already thebest-characterised coral at themolecular level and has yieldedimportant insights into theevolution of all animals”, explainsProfessor Miller who, together withDr Eldon Ball of the AustralianNational University (ANU), willlead the Acropora millepora genomesequencing program.Professor David Miller.Photo courtesy of the ARCCentre of Excellence for CoralReef StudiesCoral in the Soloman Islands. Photo courtesy of Dr Simon Foale“Corals are among the simplest animals and may reflect theancestral animal condition and reveal important features ofgenome evolution”, says Professor Miller.The project is expected to provide significant insights intothe mechanisms that underlie the evolution of life on Earth,including the genetic branch leading to the higher animalsand humans.As to why a coral has been chosen as the first Australiananimal to be gene-mapped by Australian scientists, ProfessorMiller explains: “Corals have iconic significance for Australia.We have the best-preserved coral reef system in the world andthe Great Barrier Reef is a cornerstone of a $6 billion a yeartourism industry. As reefs elsewhere in the world decline, thisvalue will grow if we can keep our reefs healthy and intact.”Continued on page 7…“ As the world’s largest reef and one of the most importantmarine ecosystems on earth, the Great Barrier Reef is oneof Australia’s greatest natural assets and national icons.”Discovery • Spring 2009 • Page 62009 annual report 31

Continued from page 6…“This gene mapping project has both practical and scientificsignificance. It will help us to understand how corals buildreefs, and why they fail to do so when they are under stress.“It will enable us to predict, with much greater confidence,how corals are likely to respond to changes in the oceans suchas warming, acidification, the spread of coral diseases, andvarious forms of pollution.”The mapping of the coral genome is a joint undertaking bythe ARC Centre of Excellence for Coral Reef Studies andthe Australian Genome Research Facility, in collaborationwith the ANU, The Walter and Eliza Hall Institute, andThe University of Queensland.“This is a fabulous example of a multi-nodal collaborationamong many players, creating a new world-class researchprogram in coral reef genomics”, says Centre Director andARC Federation Fellow, Professor Terry Hughes.The sequencing project builds on earlier collaborationsbetween the ANU and James Cook University, sponsoredby the ARC Special Research Centre for the MolecularGenetics of Development under the Directorship ofProfessor Robert Saint.Future plans for the Centre include mapping the genomeof the coral’s symbiotic partner, the dinoflagellateSymbiodinium—a primitive marine plant, with its associatedmicrobes. Symbiodinium is essential for coral growth becauseit carries out photosynthesis and provides the coral withcarbohydrates and energy.A bacterial community is also important for the health ofthe coral animal. Only by understanding all communityinteractions, and how they change under conditions ofstress, will we be able to understand how the entire coralorganism functions.For more information contact Professor Terry Hughes atterry.hughes@jcu.edu.au or on + 61 7 4781 4000.Great Barrier Reef corals. Photos courtesy of the ARC Centre ofExcellence for Coral Reef Studies32 ARC Centre of Excellence for Coral Reef Discovery Studies• Spring 2009 • Page 7

Researcher ProfileProfessor Peter MumbyThe ARC Centre welcomes newmember Professor Peter Mumby, whowill be moving to Australia from the UKin early 2010, following the award of aprestigious Laureate Fellowship. Peter’saward brings the number of seniorfellows in the Centre to four – followingthe earlier awards of a FederationFellowship (Terry Hughes, 2007-2012),Queensland Premier’s Fellowship(Ove Hoegh-Guldberg, 2008-2012) andWestern Australian Premier’s Fellowship(Malcolm McCulloch, 2009-2013). In2009, the Centre also hosts nine otherfull-time ARC Fellows, ranging across theentire spectrum of career stages.Before embarking on a research career,Peter Mumby spent two years designingmarine reserves in Belize where heexperienced, first hand, the limitedscientific basis for such planning. Thisexperience was highly influential indefining and driving his research, whichhas been dedicated to conducting appliedscience in support of the management ofcoral reefs. In 1997, he obtained his PhDin coral reef remote sensing and thenused two post-doctoral fellowships tobroaden his expertise into empirical reefecology and ecological modeling. Today,Peter uses remotely-sensed data toscale up ecological models so that theyare spatially-realistic and able to informconservation decisions directly.Peter’s research has responded to thechallenge of obtaining credible evidenceof human impacts at appropriate scales.Using remote sensing and field survey,he designed a study across Belizeand Mexico that allowed his teamto test hypotheses on the effects ofmangroves on reef fish communitystructure. An absence of mangrovescaused local extinction of the largestherbivorous fish in the Atlantic, andcaused profound reductions in thebiomass of many fish species.Peter and colleagues have also studiedthe impacts of marine reserves onCaribbean reefs and discovered thatthe direct effects of protecting fish canhave profound indirect effects on theecosystem. For example, a recoveryof parrotfish inside a well-managedreserve led to a reduction of macroalgaeand concomitant increase in coralrecruitment. Thus, while the reservebenefits fish directly, the resulting trophiccascades also benefit the corals andtherefore help ensure the delivery of reefbasedecosystem services.Peter has recently developedmechanistic ecological models of coralreefs that integrate reef dynamics,conservation actions and disturbance,including climate change. So far, themodels have provided insight into theconsequences of conserving herbivorousfishes, reducing nutrient runoff,conserving mangroves, and restoringurchin populations. These results haveinfluenced reef management policy andled to new fisheries regulations.Peter’s move to the University ofQueensland early in 2010 will allow himto forge new collaborations in Australia.His work aligns closely with the ARCCentre’s Programs 2 and 6.2009 annual report 33

GRADUATE TRAININGIn 2009, one hundred and fifty ninegraduate students were supervised bythe ARC Centre’s senior researchers,making the Centre the world’s largestprovider of graduate training in coralreef science. This commitment topostgraduate training entails a largeinvestment in support of studentresearch projects, conservatively costedat 25% of our annual budget. In addition,the Centre has a major early-careerdevelopment program. As part of this,we actively involve students through astudent committee. The Centre providesintellectual, organisational and financialhelp for student mentoring activities,student awards, inter-nodal supervisionand visits by postgraduate students.The inaugural recipients of the “TheVirginia Chadwick Awards”, are DavidAbrego, Peter Cowman, Andrew Hoey,Ruth Reef and Alejandro Reyes. The fiveprizes of $1000 are made each year foroutstanding publications written by ARCCentre of Excellence graduate students.In 2009, the ARC Centre again organisedand sponsored a National MentoringDay for student delegates attending theannual Australian Coral Reef Societymeeting. This year the mentoring daywas held at the Novotel Hotel in Darwinat the end of September. The graduatestudents who attended came fromJames Cook University, University ofQueensland, Victoria (NZ), Murdoch,Southern Cross, Sydney and NSWuniversities. An exit survey of thestudents revealed the success of theworkshop with a rating of 3.89 from apossible 4. In Brisbane, earlier in theyear at the Centre’s annual Symposium,17 graduate students participated in aworkshop entitled Talking science withthe media, organised by the Centre’sStudent Committee. The workshop waspresented by Econnect CommunicationsPty Ltd., who have for the past 15 yearsrun workshops on communicatingscience via the media.The success of the ARC Centre’sgraduate program can be seen throughthe national and international recognitionthe students attracted in 2009:• Vanessa Adams was awarded the SirKeith Murdoch Fellowship of $25,000from the American AustralianAssociation. In addition she receivedthe Ecological Society of AustraliaThe Nature Conservancy AppliedConservation Award for 2009.• Darren Coker, Rebecca Lawton,Andrew Cole and Alexander Vail wereall granted John Glover Travel Awardsby the Australian Society for FishBiology. Darren also won an AIMS@JCU conference Travel Prize.• Stephanie Januchowski receivedthree grants for conference traveland research, including $33,000 fromBiosecurity Queensland for researchassociated with her PhD studies.• Alexander Vail won the Michael HallAward for Student Innovation andthe Gilbert Whitley Memorial StudentAward (junior) at the Indo Pacific FishConference in Freemantle in June.• Andrew Cole was awarded theUniversity Centenary Student Grantfor 2009 by the Wildlife PreservationSociety of Australia,• Rebecca Fox was awarded theAustralian Coral Reef Society’s TerryWalker Prize for 2009.• At the annual Australian Coral ReefSociety Meeting in Darwin, RebeccaLawton was awarded the DanielleSimmons Award for 2009, whileEmily Howells won the Vicki HarriottMemorial Student Prize for thebest student presentation. Yui Sato,Rebecca Fox and Colin Wen alsowon student presentation prizes atthe meeting.• Andrew Cole, Rebecca Lawton andAlexandra Carter received researchsupport from the PADI Foundation.• Alexandra Carter received theGBRMPA Science for ManagementAward for 2009.• Felipe Gusmao was awarded thePeter Holloway Oceanography Prizefor his presentation at the AustralianMarine Science Associationconference in Adelaide.• Christopher Doropoulos wasawarded a Queensland GovernmentSmart State PhD Scholarship.• Rebecca Fox and Alicia Crawley wereboth awarded Lizard Island DoctoralFellowships.The Centre is indebted to the 2009Student Committee for their energyand input. They, along with studentco-ordinator, Olga Bazaka, make aninvaluable contribution to the successof the ARC Centre of Excellence.Members of the committee duringthe year were Alicia Crawley (UQ),Anne Leitch (JCU/CSIRO), Juan PabloD’Olivo (ANU), Paulina Cetina Heredia(JCU/AIMS), Rachael Middlebrook(UQ), Stephanie Januchowski(JCU) and Tom Brewer (JCU).34ARC Centre of Excellence for Coral Reef Studies

Trends in the ARC Centre’s training activities 2005 to 200920018020052006Number of students160140120100806020072008200940200PostgraduateCompletionsMulti-InstitutionalSupervisorsGraduates/Honoursstudents enrolled The ARC Centre’s international network of graduate students. In 2009, 102 overseas students, representing halfof 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 StudiesStudentUniversityCountryof OriginThesis TitleCoE Supervisor/sRene AbesamisJCU, SillimanUniversityPhilippinesDemographic connectivity of reef fish populationsin the Philippines. (PhD)Prof G Russ, Prof G JonesDavid Abrego JCU, AIMS Mexico Temporal and environmental influences on theearly establishment and maintenance of coral-Symbiodinium symbioses. (PhD awarded)Vanessa Adams JCU USA Incorporating economic factors into systematicconservation planning. (PhD)Siham Afatta UQ Indonesia Human impacts, resilience and managementchallenges for Indonesian coral reefs:Karimunjawa National Park case study. (MSc)Campbell Allen UQ Australia Australian eco-informatic tools for coral reefecology. (MSc)Jorge Alvarez-Romero JCU Mexico Cross-system threats and competing valuesin coastal and marine conservation planning:an integrated land-sea approach to prioritizeconservation actions in the Gulf of California.(PhD)Shelley Anthony JCU, AIMS USA White Syndrome Disease and colony mortality incaptive Indo-Pacific corals. (PhD)Stephen Ban JCU Canada Investigating resilience and spatial responsesof coral reef ecosystems to climate change andassociated stressors. (PhD)Lissa Bar UQ, JCU Australia Measuring the effectiveness of marine protectedareas. (PhD)Prof B Willis, Dr M vanOppen, Prof S ConnollyProf R Pressey,Prof T HughesDr K Anthony,Prof O Hoegh-GuldbergProf O Hoegh-GuldbergProf R Pressey,Dr N Ban, Dr J KoolProf B WillisProf R Pressey,Dr N Graham,Prof S ConnollyProf R PresseyChristopher Bartlett JCU USA Marine conservation in Vanuatu. (PhD) Dr J CinnerBrian Beck UQ, JCU USA Palaeoecological dynamics of coral communitiesalong a disturbance gradient, Solomon Islands.(PhD)Prof J Pandolfi,Prof S ConnollyRoger Beeden JCU NewZealandHow healthy is the Great Barrier Reef in awarming world? (PhD)Prof B WillisVictor Beltran-Ramirez JCU Mexico Molecular aspects of the fluorescent proteinhomologues in Acropora millepora. (PhD)Dorothea Bender UQ Germany Impacts of climate change on macroalgae andtheir interactions with coral reef organisms. (PhD)Rose Berdin ANU Philippines Late Quaternary Palaeoclimate history of thenorthern Indo-Pacific warm pool from raised coralreefs in the Philippines. (PhD awarded)Prof D MillerDr G Diaz-Pulido,Dr S DoveProf M McCullochDuan BiggsJCU, CSIRSouth Africa,EmoryUniversityUSA,University ofCanterbury NZSouth AfricaResilience of reef-based tourism to climatechange and disturbance. (PhD)Prof T Hughes, Dr J CinnerTeressa Bobeszko JCU Australia The role of carbonic anhydrase in the coraldinoflagellatesymbiosis. (PhD)Lynda Boldt JCU Australia Symbiodinium photosynthetic genes and theeffect of varying environmental conditions onphotosynthetic processes. (PhD)Dr W Leggat,Prof D YellowleesDr W Leggat,Prof D YellowleesRoberta Bonaldo JCU Brazil The ecosystem role of parrotfishes. (PhD) Prof D Bellwood,Prof S Connolly36ARC Centre of Excellence for Coral Reef Studies

StudentUniversityCountryof OriginThesis TitleCoE Supervisor/sPim Bongaerts UQ Netherlands Ecological significance of deep, light-dependentcoral communities. (PhD)Mary Bonin JCU USA Causes and consequences of habitatspecialization in coral reef fish communities.(PhD)Prof O Hoegh-GuldbergProf G Jones, Dr G AlmanyMadeleine Bottrill UQ, JCU UnitedKingdomEvaluating the effectiveness of conservationplanning: when do plans work. (PhD)Prof R PresseyTom Brewer JCU, UQ Australia Linking sociological perspectives to coral reefresources across scales. (PhD)Kate Bromfield UQ, CSIRO Australia Neogene corals of the Indo-Pacific. (PhDawarded)Prof T Hughes,Prof R Pressey, Dr J Cinner,Dr S Foale, Prof J PandolfiProf J PandolfiRohan Brooker JCU NewZealandReproduction and ecology of the harlequinfilefish, Oxymonacanthus longirostris, and theimplications of climate change. (MSc)Prof G Jones,Prof P MundayMichael Cappo JCU, AIMS Australia Spatial patterns of demersal vertebrateassemblages in inter-reef waters. (PhD)Alexandra Carter JCU Australia The effects of no-take zoning, region and year onreproductive output of the common coral trout,Plectropomus leopardus. (PhD)Paulina Cetina-Heredia JCU, AIMS Mexico Modelling physical and biological processesdriving laval transport and supply in reef systems.(PhD)Neil Chan JCU, UQ Malaysia Modelling the effects of pH, temperature andflow on calcification of reef corals. (PhD)Rowan Chick JCU Australia Stock enhancement of local populations ofblacklip abalone Haliotis rubra in New SouthWales, Australia. (PhD)Chia-Miin Chua JCU Malaysia Effects of elevated temperature and increasedacidity on the early life history of coral. (PhD)Tara Clark UQ, AIMS Australia Dating and mapping historical changes in GreatBarrier Reef coral communities. (PhD)Philippa Cohen JCU Australia The contribution of locally-managed marine areasto food security of Solomon Islands. (PhD)Prof M KingsfordDr M McCormick,Prof G RussProf S ConnollyProf S Connolly,Dr K AnthonyProf M KingsfordDr A Baird, Dr W Leggat,Prof T HughesProf J PandolfiDr S Foale, Prof T HughesDarren CokerJCU, DEC inWA, AIMSNewZealandThe role of live coral in moderating key ecologicalprocesses for coral reef fishes. (PhD)Dr M Pratchett,Dr N GrahamAndrew ColeJCU, DEC inWAAustraliaThe effect of chronic fish predation onscleractinian corals. (PhD)Dr M Pratchett,Prof G JonesMelissa Cowlishaw JCU Australia Determinants of home range and territorialbehaviour in coral fishes: roles of body size,habitat structure and population density. (PhD)Peter Cowman JCU Ireland Dating the evolutionary origins of trophic noveltyin coral reef fishes. (PhD)Alicia Crawley UQ Australia The synergistic effect of rising ocean temperatureand acidification on coral reef ecosystems. (PhD)Vivian Cumbo JCU, AIMS Australia Thermal tolerance in corals: the role of thesymbiont. (PhD)Kathryn Danaher JCU Australia Oceanography and the condition of plankton.(PhD)Prof G Jones,Dr M McCormickProf D BellwoodDr S Dove, Dr S DunnDr A Baird, Dr M vanOppen, Prof T HughesProf M Kingsford2009 annual report 37

StudentUniversityCountryof OriginThesis TitleCoE Supervisor/sAndrea de Leon ANU Australia Palaeoceanographic records of the SouthernOcean: insights from the boron composition ofbiogenic silica. (PhD)Prof M McCullochJeffry DeckenbackUQ, JCU,MonashUSAMaturation, turn-over, oligomerization, andtransport of pocilloporins. (PhD awarded)Dr S Dove, Dr W LeggatBrynn Devine JCU USA Effects of ocean acidification on habitat selectionin fish. (MSc)Ayax Diaz-Ruiz UQ Mexico The use of coral associated fauna as indicators ofcoral health. (PhD)Danielle Dixson JCU USA Use of olfactory cues for settlement site selectionin coral reef fishes. (PhD)Juan Pablo D’Olivo ANU Mexico Environmental and climate variability in seawaterpH reconstructed from Boron isotopes in coralsfrom the Pacific Ocean. (PhD)Jennifer Donelson JCU, CSIRO Australia Climate change and the future for coral reeffishes: impacts and adaptation. (PhD)Christopher Doropoulos UQ Australia Climate change effects on the recruitment andsuccession of algae and corals from the GreatBarrier Reef. (PhD)Maxi Eckes UQ Germany How do coral reef fish protect themselves fromsolar ultraviolet radiation? (PhD)Udo Engelhardt UQ Australia Community-level ecological responses of coralreef biota to mass coral bleaching events. (PhD)Richard Evans JCU Australia No-take marine protected areas: abundance,biomass, batch fecundity and genetic connectivityof target species on the Great Barrier Reef. (PhDawarded)Michael Fabinyi ANU, JCU Australia Fishing for fairness: poverty, morality and marineresource regulation in the Calamianes Islands,Philippines. (PhD awarded)Kar Hei (James) Fang UQ China The synergistic effects of ocean warming andacidification on growth and bioerosion capacity ofthe marine sponge Cliona orientalis, on the GreatBarrier Reef, Australia. (PhD)Prof P Munday,Prof G JonesProf O Hoegh-Guldberg,Prof J PandolfiProf P Munday, Prof GJones, Dr M PratchettProf M McCullochProf P Munday,Dr M McCormickDr Guillermo Diaz-PulidoDr S DoveProf O Hoegh-GuldbergProf G Russ, Prof G JonesDr S FoaleDr S Dove,Prof O Hoegh-GuldbergPepito (Sonny)FernandezANU, JCU Philippines Political engagements in marine protected areagovernance in northeastern Liloilo, Philippines.(PhD)Dr S FoaleRebecca Fox JCU UnitedKingdomEcosystem function of rabbitfishes (F:Siganidae)on the Great Barrier Reef, Australia. (PhD)Prof D BellwoodMatthew Fraser JCU Australia Dynamics of egg predation at tropical fishspawning sites. (PhD)Irene Fuertes Jerez JCU Spain Characterization of microsatellite loci forEpinephelus quoyanus (epinephelinae): preparingto measure connections from no-take to fishedareas of the Great Barrier Reef. (MAppSc)Dr M McCormick,Prof G JonesProf G Russ, Prof G JonesNaomi Gardiner JCU Australia Habitat specialization, co-occurrence and restingsite fidelity in cardinalfish on coral reefs. (PhD)Prof G JonesChris Goatley JCU UnitedKingdomThe ecological role of sediments on coral reefs.(PhD)Prof D Bellwood38ARC Centre of Excellence for Coral Reef Studies

StudentUniversityCountryof OriginThesis TitleCoE Supervisor/sAlonso Gonzalez-CabelloJCU Mexico Cryptobenthic reef fish ecology in the GreatBarrier Reef, Australia. (PhD)Prof D BellwoodLuis Gonzalez ReynosoJCU, GriffithUniversityMexicoMechanisms of stress inhibition of reproductionin fish. (PhD)Dr M McCormickLauretta Grasso ANU, JCU Australia Transcriptome analysis of development, with afocus on metamorphosis, in the coral Acroporamillepora. (PhD awarded)Erin Graham JCU USA Energetics of coral larvae and its implications fordispersal. (PhD)Jessica Haapkyla JCU, AIMS Finland Impacts and drivers of coral disease in Indo-Pacific reefs. (PhD)Andrew Halford JCU Australia Disturbance, habitat structure and coral reef fishcommunities. (PhD)David Harris UQ Australia Ecology of high latitude populations ofPomacentrus coelestis. (PhD)Prof D MillerProf B Willis, Prof SConnolly, Dr A BairdProf B WillisProf G JonesProf O Hoegh-GuldbergHugo HarrisonJCU, Universityof PerpignanFranceLarval recruitment dynamics and the geneticstructure of coral reef fish populations in marineprotected networks. (PhD)Prof G Jones, Prof G Russ,Dr S PlanesMeegan Henderson UQ Australia Microbial ecology of coral disease: the use ofmolecular techniques in understanding bacterialcommunity shifts. (PhD awarded)Prof O Hoegh-GuldbergChristina Chemtai Hicks JCU UnitedKingdomThe interplay between economic values andsocietal settings in coral reef governance. (PhD)Prof T Hughes, Prof RPressey, Dr J E CinnerJean-Paul Hobbs JCU Australia Isolation, endemism and the structure of coralreef fish communities on islands. (PhD)Prof G Jones, Prof PMundayAndrew Hoey JCU Australia Algal-fish interactions on coral reefs. (PhD) Prof D Bellwood,Prof G RussThomas Holmes JCU Australia Selectivity of predation on newly settled tropicalreef fish. (PhD)Emily Howells JCU, AIMS Australia Genetic resilience of Symbiodinium populations:the role of coral endosymbionts in reef adaptationto climate change. (PhD)Stephanie Januchowski JCU USA Towards stream classifications for conservationplanning: a Wet Tropics region case study. (PhD)Jacob Johansen JCU Denmark Energetics of habitat choice in planktivorous coralreef fishes. (PhD)Charlotte Johansson JCU, AIMS Sweden Managing coral reefs - the importance of workingwith functional groups to conserve ecosystemresilience. (PhD)David Jones JCU Australia Predicting the distribution of two venomouscubozoans (Carukia barnesi and Chironex fleckeri)using population genetic structure. (PhD)Jung Ok Kang ANU Korea Anthropogenic increase of atmospheric carbondioxide and ocean acidification and globalwarming: implications for long-term changes inthe calcification rate of coral reefs. (PhD)Rucha Karkarey JCU India Using northern and southern Great Barrier Reefgreen turtle (Chelonia mydas) nesting data as aproxy to estimate abundance of the remote CoralSea nesting population. (MAppSci)Dr M McCormickProf B Willis, Dr L Bay,Dr M van OppenProf R PresseyProf G Jones,Prof D BellwoodProf D BellwoodProf M Kingsford,Prof G RussProf M McCullochProf S ConnollyBrent Knack JCU Australia Cell adhesion factors in Cnidarians. (PhD) Prof D Miller, Dr W Leggat2009 annual report 39

StudentUniversityCountryof OriginThesis TitleCoE Supervisor/sValeriya Komyakova JCU Russia Habitat characteristics as the determinants ofthe local diversity and structure of coral reef fishcommunities. (MSc awarded)Prof G Jones,Prof P MundayNarinratanaKongjandtreUQ Thailand The taxonomy and systematics of the genusFavia from Thai waters. (PhD)Prof O Hoegh-GuldbergCharlotte Kvennefors UQ, JCU Sweden Host-microbe interactions in reef-building corals.(PhD awarded)Joleah Lamb JCU USA Effects of offshore tourist pontoons on coraldisease prevalence in the Cairns and Whitsundaysectors of the Great Barrier Reef Marine Park.(MAppSc)Angela Lawton UQ USA The effects of micro-scale variation on thephotosynthetic productivity of the symbiotic algaeof reef building corals. (PhD)Dr W Leggat,Prof O Hoegh-GuldbergProf B WillisProf O Hoegh-Guldberg,Dr S DoveRebecca Lawton JCU, KAUST NewZealandGeographic variation in the ecology ofbutterflyfishes and resilience to large scaledisturbances. (PhD)Dr M Pratchett, Dr L Bay,Prof T HughesHelene Le Grand JCU, AIMS France Development of coral bioindicators to detectchanges in water quality on inshore reefs of theGreat Barrier Reef. (MAppSc)Prof B WillisCarine Lefevre JCU France The ecology of cryptobenthic reef fishes. (PhD) Prof D BellwoodAnne Leitch JCU, CSIRO Australia Social resilience to climate change: the adaptivecapacity of local government. (PhD)Prof T HughesAnais Kimberley Lema JCU, AIMS Mexico/FranceNitrogen fixing bacteria associated with corals ofthe Great Barrier Reef. (MSc)Prof B WillisTove Lemberget JCU Norway Importance of body condition and growth to larvalsurvival of a Caribbean lizardfish. (PhD)Dr M McCormick,Prof G JonesVetea Liao JCU FrenchPolynesiaDirect effect of temperature on growth and bodycondition of the coral reef fish Acanthochromispolyacanthus. (MAppSc)Dr M PratchettRaechel Littman JCU, AIMS USA The dynamics of bacterial populations associatedwith corals and the role of bacterial pathogens incoral bleaching. (PhD)Adrian Lutz JCU, AIMS Switzerland Coenzyme Q and Plastoquinone redox balance asa physiological determinant of oxidative stress incoral algal symbiosis. (PhD)Matt Lybolt UQ USA Causes of change in coastal ecosystems: past,present and future. (PhD)Prof B WillisProf D Miller,Dr M van OppenProf J PandolfiThomas Mannering JCU UnitedKingdomDo marine reserves augment recruitment innearby fished areas? (MSc awarded)Prof G JonesJeffrey MaynardU. Melbourne,UQUSAClimate-change processes affecting coral reefecology. (PhD)Dr K AnthonyDominique McCowan JCU USA Bleaching susceptibility of corals: a hierarchy ofcauses and consequences. (PhD)Amelie Menchenin JCU France Early life history of Epinephelus quoyanus.(MAppSc)Dr M Pratchett, Dr A Baird,Prof T HughesProf G Jones, Prof G RussLuiz- Felipe Mendes-de-GusmaoJCU, AIMS Brazil Studies on secondary production of zooplanktonin tropical seas and aquaculture. (PhD)Prof M KingsfordVanessa Messmer JCU, U.PerpignanFranceCauses and consequences of declining fishbiodiversity in coral reefs. (PhD)Prof G Jones,Prof P Munday40ARC Centre of Excellence for Coral Reef Studies

StudentUniversityCountryof OriginThesis TitleCoE Supervisor/sRachael Middlebrook UQ Australia Determining thermal threshold dynamics andvariability in reef building corals. (PhD)Dr S Dove, Dr K Anthony,Prof O Hoegh-GuldbergGabrielle Miller JCU Australia Impact of pH on fish development. (PhD) Prof P Munday,Dr M McCormickMorena Mills JCU Brazil Implementation opportunity in systematicconservation planning. (PhD)Prof R Pressey,Dr N Ban, Dr S FoaleMatthew Mitchell JCU UnitedKingdomAntipredator defence through chemical alarmcues - how common amongst tropical marinefishes? (PhD)Dr M McCormickRoshni Narayan UQ Canada Holocene to recent changes in the benthicforaminifera communities of subtropical MoretonBay, Queensland and potential indicators formonitoring sediment/water quality in estuarineenvironments. (PhD)Crystal Neligh JCU USA Links between metabolism, growth andperformance (MSc)Daisie Ogawa JCU USA Synergistic effects of ocean acidification andelevated temperature on carbon-concentratingmechanisms and energy transfer in the coralholobiont. (PhD)Juan Carlos Ortiz UQ Venezuela Eco-physical dynamics of the Heron Island coralreef. (PhD)Cathie Page JCU Australia Ecology and biology of coral diseases on theGreat Barrier Reef. (PhD awarded)Allison Paley JCU, AIMS USA Genetic diversity, bleaching sensitivity and colourpolymorphisms of a common reef-building coral,Acropora millepora, on the Great Barrier Reef,Australia. (MSc)Prof J PandolfiDr M McCormickDr W Leggat,Prof D YellowleesProf O Hoegh-GuldbergProf B Willis, Prof THughesProf B Willis,Dr M van OppenCaroline PalmerJCU,NewcastleUniversityUnitedKingdomThe basic biological mechanisms of scleractinianimmune defences involved in wound healing anddisease mitigation. (PhD)Prof B WillisChristine Pam JCU Australia Social responses to change on small islands inMicronesia. (PhD)Dr S FoaleJoe PollockJCU , AIMS,College ofCharlestonUSAPhylogeography of the coral pathogen, Vibriocoralliilyticus, and the development of a qPCRbaseddiagnostic assay for its detection. (MSc)Prof B WillisMary Portwood JCU USA Influence of marine protected areas oninvertebrate communities. (MAppSc)Eneour Puill-Stephan JCU, AIMS France Self-nonself recognition and chimerism inAcropora millepora. (PhD)Prof G JonesProf B Willis,Dr M van OppenPaola G. Rachello-DolmenUQ Italy Constructing long-term proxy records of historicalchanges in marine mollusc assemblages intropical and subtropical Queensland region(Australia). (PhD)Prof J PandolfiJean-Baptiste Raina JCU, AIMS France Coral-associated bacteria and their role in thebiogeochemical cycle of sulphur. (PhD)Prof B WillisAna Redondo-RodriguezUQ, AIMS Spain Implications of climate change for theoceanography of the Great Barrier Reefecosystem. (PhD)Dr K Anthony,Prof O Hoegh-GuldbergRuth Reef UQ, JCU Israel The effect of temperature on the accumulationand repair of UV damage in zooxanthellae andcorals. (PhD awarded)Prof O Hoegh-Guldberg,Dr W Leggat, Dr S Dove2009 annual report 41

StudentUniversityCountryof OriginThesis TitleCoE Supervisor/sAlejandro Reyes JCU Colombia Cellular mechanisms of coral calcification. (PhD) Prof D MillerCatalina Reyes UQ Colombia The role of elevated CO2 scenarios on bioerosionof coral reef ecosystems. (PhD)Dr S Dove,Dr G Diaz-Pulido,Prof O Hoegh-GuldbergMaria Catalina Reyes-NiviaUQ Colombia Effects of climate change on bioerosion of reefcarbonates. (PhD)Dr S Dove,Dr G Diaz-PulidoClaire Reymond UQ, AIMS Australia Modern evolutionary and palaeoecology offoraminifera from the Great Barrier Reef:establishing a baseline. (PhD)Zoe Richards JCU, AIMS Australia Characteristics of rare and common corals:implications for conservation. (PhD)Alma Ridep-Morris JCU Palau Dynamics of coral diseases on Palauan reefs andthe role of marine protected areas in mitigatingtheir impacts (MSc)Jairo Rivera Posada JCU Colombia Pathogenesis in crown-of-thorns starfish(Acanthaster planci). (PhD)Prof J PandolfiProf D Miller, Prof B Willis,Dr M van OppenProf B Willis, Prof G JonesDr M Pratchett, Prof THughes, Dr T AinsworthGeorge Roff UQ UnitedKingdomHistorical ecology of coral communities from theinshore Great Barrier Reef, Australia. (PhD)Prof J Pandolfi,Prof O Hoegh-GuldbergPablo Saenz-Agudelo JCU ,University ofPerpignanColombiaDemography and connectivity in coral reef fishpopulations as revealed by parentage analysis.(PhD)Prof G JonesYui Sato JCU, AIMS Japan Dynamics of a black band disease outbreak.(MSc)Shio Segi ANU, JCU Japan Living under threat: depletion, development andmarine protected areas in the lives of small-scalefishers in the Philippines. (PhD)Prof B WillisDr S FoaleFrancois SenecaJCU, AIMS,ANUMonacoThe molecular stress response in a modelscleractinian coral: Acropora millepora. (PhD)Prof D Miller,Dr M van OppenMichael Short JCU Australia The recovery of coral reefs following shipgrounding disturbances. (MSc)Jennifer Smith JCU Canada Influence of patch dynamics on coral reef fisheson the southern GBR. (MSc)Prof B Willis, Prof G JonesProf G Jones,Dr M McCormickJessica StellaJCU, AustralianMuseumUSAClimate impacts on non-coral reef invertebrates.(PhD)Prof G Jones, Dr MPratchett, Prof P MundayMeir Sussman JCU, AIMS Israel A molecular approach to the study of coraldiseases. (PhD awarded)Jill Sutton ANU Canada Southern ocean nutrients and climate change:insights from isotopic and elemental signatures ofdiatoms and sponges. (PhD)Chun Hong Tan JCU Malaysia Environmental controls and evolutionaryconstraints on growth and reproduction in corals.(PhD)Michelle Templeman JCU Australia The role of jellyfish in cycling contaminantsin the marine environment and their utility asbiomonitors. (PhD)Prof B WillisProf M McCullochDr A Baird, Dr M Pratchett,Dr L BayProf M KingsfordLoic ThibautJCU,UniversitéPierre et MarieCurieFranceResilience in coral reef and model ecosystems.(PhD)Prof S Connolly,Prof T Hughes42ARC Centre of Excellence for Coral Reef Studies

StudentUniversityCountryof OriginThesis TitleCoE Supervisor/sLucija Tomljenovic JCU Croatia Charcterisation of the TTC4 gene family. (PhDawarded)Gergely Torda JCU, AIMS Hungary Assessment of ecological connectivity in corals:implications for their recovery from majorperturbations and their potential to adapt toclimate change. (PhD)Mélanie Trapon JCU France Ongoing disturbances and further shifts incommunity structure among coral assemblagesat Moorea, French Polynesia. (MAppSc)Lubna Ukani JCU India Characterisation of DNA methylation systems inAcropora and other lower animals. (PhD)Prof D MillerDr M van Oppen,Prof B WillisDr M Pratchett, Dr L Penin,Prof G JonesProf D Miller, Dr W LeggatSvetlana Ukolova JCU Russia Signalling molecules in coral development. (PhD) Prof D Miller, Dr W LeggatAnnamieke Van DenHeuvelUQ, JCU Australia Characterisations of genes, proteins, and theregulatory pathways involved in nitrogen uptakeand the assimilation in Acropora aspera and itssymbiont Symbiodinium sp. (PhD)Dr S Dove, Dr W Leggat,Prof D YellowleesCameron Veal UQ Australia Meso-and micro-scale light fields around shallowcoral reefs. (PhD)Prof O Hoegh-Guldberg,Dr K Anthony, Dr S DoveAna Cecilia VillacortaRathJCU Peru Selective mortality during early life stages ofsprats. (MSc)Dr M McCormick,Dr M MeekanPiero ViscontiJCU, UniversityLa Sapienza,Rome, ItalyItalyIncorporating biodiversity processes and dynamicthreats in systematic conservation planning. (PhD)Prof R PresseyMarcelo Visentini-KitaharaJCU,SmithsonianInstituteBrazilTaxonomic and phylogenic trends amongazooxanthellate corals, using morphological andmolecular aspects. (PhD)Prof D MillerStefan Walker JCU Australia The socio-biology of life history transitions andlifetime fecundity in a tropical haremic reef fish.(PhD)Patricia Warner JCU, AIMS USA Reproductive ecology and population geneticapproaches to assessing connectivity of thebrooding coral, Seriatopora hystrix. (PhD)Christine Weaver JCU USA Competition between two damselfishes.(MAppSc)Dr M McCormick,Prof P MundayProf B Willis,Dr M van OppenDr M McCormickRebecca Weeks JCU UnitedKingdomApproaches to designing marine protected areanetworks in the Philippines. (PhD)Prof G RussYvonne Weiss JCU Germany The immune system of Acropora millepora:identification and characterisation of candidategenes. (PhD)Colin Wen JCU Taiwan Recruitment hotspots and their role in the ecologyand management of large exploited predatoryfishes. (PhD)Amelia Wenger JCU USA Effects of sedimentation and turbidity onplanktivorous fishes. (MSc)David Williamson JCU Australia Fishery effects and benefits of marine protectedareas within the Great Barrier Reef Marine Park.(PhD awarded)Huibin Zou JCU China The characterisation of selenium containingprotein families in coral Acropora millepora. (PhD)Prof D Miller, Dr W Leggat,Dr T AinsworthProf G Jones, Dr MPratchett, Dr G AlmanyProf G Jones,Dr M McCormickProf G Russ, Prof G JonesProf D Miller,Dr T Ainsworth2009 annual report 43

Media and Public OutreachThe ARC Centre seeks to informthe wider community of its researchoutcomes through the media andthrough public awareness activities. In2009, Centre personnel participated in45 public outreach programs, reachingaudiences locally, nationally andinternationally. Examples include:• Researchers from the ARC Centre ofExcellence teamed with Google topopulate the GBR section of GoogleEarth’s Ocean with information aboutthe reef and human impacts on it.• The Centre hosted its 2-day nationalsymposium and public forum inBrisbane on the 6 th – 7 th August• Under the Queensland Scientists inSchool program, Line Bay, hostedan information booth about threatsto the Great Barrier Reef at theMundingburra State School 125 th yearanniversary fete.• At the invitation of the RoyalAustralasian College of Surgeons,John Pandolfi presented a lectureCountdown to extinction: Can coralreefs survive?• Terry Hughes presented apublic lecture in Brisbane oncoral reef resilience, part of alecture series run by the NationalClimate Change AdaptationFacility, at Griffith University.• In association with the Queenslandbranch of the Australian Academyof Science, the Centre hosted apublic forum in Townsville, withpresentations from six Fellows of theAcademy, including Terry Hughes andAcademy medallist Sean Connolly, toshowcase the growing internationalprofile of Queensland scientists.• Malcolm McCulloch presented alecture Shaping the Future ClimateChange: Sceptics Denial as part ofthe University of Western Australia’spublic lecture series.• During October and November, MikeKingsford gave a series of publiclectures at the University of Bergen(Norway), University of Copenhagen(Denmark) and the University ofUppsala (Sweden).• Ove Hoegh-Guldberg participated ina Q&A session at the internationallaunch in Copenhagen of the moviedocumentary A Sea Change: imaginea world without fish.• In Kimbe Bay, Papua New Guinea,Glenn Almany led a series ofdiscussions with local communitiesthat own, manage and depend oncoral reefs about climate change,overfishing and the value of marineprotected area networks in mitigatingtheir impacts and the importance ofunderstanding connectivity to designa resilient network.• In April, Josh Cinner participatedin a public forum on Beyond theobituaries: success stories in marineconservation at the SmithsonianInstitute in Washington DC.As part of our communications strategythe Centre has developed a robustmedia strategy in consultation withJulian Cribb, our media advisor. Julianconverts sometimes esoteric scienceinto everyday language and delivers ourresearch findings to a diverse Australianand international audience.In 2009, the ARC Centre produced 39media releases, generating 2190 mediastories that reached local, national andinternational audiences. Five hundredand eighty-four news articles andcommentaries were on the web, inaddition to 71 television and 296 radioreports, 1073 newspaper and 166magazine articles. The Centre’s researchin the Coral Triangle region attractedconsiderable media coverage during theWorld’s Ocean Conference in Manado,Indonesia in May 2009. Over 900 mediastories were generated during the weeklong conference (see p.46).The Centre’s website caters for multipleaudiences, providing information, accessto resources, research services, anddownloads of research, teaching andeducational tools. The site received4.5 million web hits in 2009, a six-foldincrease over the past 4 years. It ranksfirst of 20.2 million websites found in aGoogle search for “coral research”.In 2009, the Centre’s educationalresources web pages were furtherdeveloped to cater for the demandby school children for information oncoral reefs. In collaboration with theAustralian Academy of Science, a newNOVA topic, Science for sustainablereefs, was developed and launched onthe Academy’s website. This resourceprovides the latest science on coralreefs in a format readily accessible forsecondary school teachers, studentsand parents. The Centre’s highlypopular webinar series continued in2009 with the addition of 35 new talksunder the theme, Securing the Futureof Coral Reefs. These videos rangefrom short, highly topical presentationson issues of interest to a generalaudience to longer videos showcasingthe latest, leading-edge science for ascientifically informed audience. TheCentre also developed a new websitefor the 2012 International Coral ReefSymposium which will be launched inMarch 2010. During 2010, the Centre’swebsite will be redesigned to enhanceaccess to our research services andinformation, and to improve navigability.44ARC Centre of Excellence for Coral Reef Studies

Examples of the Centre’s2,190 media hits in 2009include:New Scientist, Acid oceans no laughingmatter for clownfish, 2/2/09, P.MundayBBC News, Australian scientists havefound a new, unexpected impact ofocean acidification, 4 /2/09, P MundayAustralian Story, ABC television. The heatof the moment, 9/2/09, O Hoegh-GuldbergThe Australian, Barrier Reef lands inGoogle Net, 11/2/09, D BellwoodCNN.com/Asia, Beating poverty wouldsave coral reef fish, 9/2/09, J CinnerBush Telegraph, ABC Radio National,Fat corals make better survivorsinterview, 10/3/09, K AnthonyConservation Magazine, Saving Nemo,24/3/09, G JonesLateline, ABC television, interview withMargot O’Neill, 30/3/09, O Hoegh-GuldbergThe Guardian, UK, Damaged Barrier Reefcoral makes ‘spectacular’ recovery,22/4/09, G Diaz PulidoDiscovery Channel, Stress gives fishwonky ears, 28/4/09, M McCormickSolomon (Islands) Star, Markets depletefish stocks here, 29/4/09, T BrewerABC local and national news, Coralcan’t escape the heat, 7/5/09, MMcCullochThe Jakarta Post, Oceans key in climatechange battle, 14/5/09, O Hoegh-GuldbergThe Reef and Marine Aquariummagazine, The Lazarus Reef:rebounding bleached Acropora coralsrecorded off Australia, May/June09, K Anthony, M Hoogenboom, RMiddlebrookSydney Morning Herald, Scientistswarn acid is killing oceans, 2/6/09, THughesThe Hindu, Failed policies, corruptionleading to overfishing, 23/6/09, JCinnerWorld News, World’s corals face dangeras global warming whips up powerfulstorms, 24 June 2009, J MallelaAfrica Geographic, On the social scale,July 09, J CinnerTownsville Bulletin, Happiness doesn’thave to cost the Earth, 11/7/09, SFoaleAustralian Geographic, News: turf wars,14/7/09, L PeninScienceBlog, Humans ‘damaging theoceans’, 30/7/09, M KingsfordThe Age, Scientists to unlock GreatBarrier Reef genome, 30/7/09, DMillerBayJournal, Moreton Bay corals get thespotlight, 6/8/09, J PandolfiSunday Mail, Scientists find Nemo all atsea, 9/8/09, P MundayCourier Mail, ’TimTams’ of the reef gomissing, 25/8/09, D BellwoodCairns Sun, $14m reef forum coup,26/8/09, ARC CentreMalaysia Sun, Man-made crisesoutrunning our ability to deal withthem, 12/9/09, T HughesAustralian R&D Review, World at atipping point, October 2009, THughes7.30 report, ABC TV, Feature- coralcalcification, 10/10/09, J Lough, ACrawley, S DoveTownsville Bulletin, Bullied to death,7/11/09, M McCormickReuters, Great Barrier Reef survival‘requires 25% CO 2cut’, 17/11/09, THughesARD German public radio network,interview with Bernd MuschBorowska, 2/12/09, O Hoegh-GuldbergSeoul Times, Scientists call for ‘oceanparks’ to protect seas, 8/12/09, BPressey2009 annual report 45

Photo by Pim BongaertsAustralian NewsAUSTRALIA: Scientist Pushes ForCoral Triangle ActionWritten by Stephen de TarczynskiMELBOURNE, Jul 7 (IPS) - While Australia remainscommitted to playing an ongoing role in assisting the sixnations of the Coral Triangle Initiative (CTI) to protect theirmarine environments, a leading scientist here says that anAustralian-style of management in the triangle will not work.“There is no single recipe for how to manage a reef welland the Great Barrier Reef model is not exportable to apoor country,” says Professor Terry Hughes, director ofthe highly-regarded Australian Research Council Centreof Excellence for Coral Reef Studies. The Centre is apartnership of several leading universities and statutorybodies - located at James Cook University in Townsville.“Australia is very much the lucky country when itcomes to having the resources to manage reefs andto pay for science and reef management,” he says.“There’s a huge contrast between Australian investmentin science and reef management compared to almostanywhere else in the world because most coral reefcountries in the tropics are developing countries andjust don’t have the resources that we do,” he adds.But the signing of the declaration of the Coral TriangleInitiative on Coral Reefs, Fisheries and Food Security atthe CTI summit in Manado, Indonesia in May indicatesthat where the political will exists, less-affluent nations canalso undertake action to protect their marine environmentsfor the benefit of current and future generations.Indonesia, Malaysia, the Philippines, East Timor, PapuaNew Guinea and the Solomon Islands - the so-calledCoral Triangle Six (CT6) - have committed to cooperateto preserve the biologically diverse yet highly-populatedCoral Triangle, an area which covers some 5.7 millionsquare kilometers in Southeast Asia and Melanesia.Australia is currently involved in researching marineenvironments in the triangle and in the Pacific region,with the ARC Centre of Excellence for Coral ReefStudies working already in the Philippines, Indonesia,the Solomon Islands and Papua New Guinea.“The initiative is new and it’s wonderful to see it,but Australian scientists see this as an opportunityto ramp-up an existing engagement. It’s not asif we’re starting from scratch,” says Hughes.Additionally, of the Centre’s current batch of 155 PhDstudents, 95 are from the immediate region. Australiawas quick to pledge an initial AUD$2 million to fundcritical projects within the CTI - part of the USD$300million to be provided by the Global EnvironmentFacility, the Asian Development Bank, the United Statesand other partners. The Rudd government describes thefirst phase of this as an “ongoing plan” to back the CT6.“This investment will focus on areas where we can makethe greatest contribution by sharing our knowledge anddirectly supporting capacity building in marine biodiversityconservation, sustainable fisheries, protecting vulnerablemarine species and community empowerment,” saidPeter Garrett, the country’s environment minister.Australia’s role as a supporter of the CT6 stems from arequest sent to it by Indonesian President Susilo BambangYudhoyono at a CTI meeting in Bali in Dec. 2007. He asked forAustralian technical expertise to aid in protecting the triangle.Hughes told IPS that Australia is compelled to act.“Australia has a capacity that, in my opinion, obligates itto be a major player in the Coral Triangle region,” he said.While he supports the view that the threat faced bythe inhabitants of the triangle’s coastal areas requiresa multilateral approach, the diversity of marineenvironments within the Coral Triangle means that aone-size-fits-all solution to management is not viable.“You need to tailor-make the management style to whatwill work on the ground in the different regions,” saysHughes. Written by Stephen de TarczynskiArticle extract, reproduced with thanks to AustralianNews website www.australia.to46ARC Centre of Excellence for Coral Reef Studies

© Giles Winstanley / pelagicon.comInternational Coral ReefSymposium 2012The ARC Centre and James CookUniversity are honoured to have beeninvited by the International Societyfor Reef Studies to host the 12thInternational Coral Reef Symposium(ICRS) in Australia in 2012. The ICRS isthe world’s largest and most importantcoral reef meeting, bringing togethercoral reef scientists, educators, graduatestudents, resource managers and policymakers. The 12th ICRS is expected toattract approximately 2,500 delegatesfrom 80 countries to the CairnsConvention Centre, from 9th–13th July2012. A First Announcement was madein 2009 to inform potential delegatesof the dates and venue for the nextICRS and also to direct them to theSymposium’s new website, atwww.icrs2012.com.ICRS 2012 will provide the internationalscience community with a platform toincrease global knowledge and interestin coral reefs, as well as the opportunityto showcase innovative science, andthe latest developments in coral reefconservation and management. Close to2,000 talks and posters will be presentedon major themes including climatechange, reef ecology, conservationplanning, fish and fisheries, genomics,management tools, the Coral TriangleInitiative and the human dimension ofcoral reefs.Activities at ICRS 2012 will include acomprehensive science program, a tradeexhibition, and field trips both beforeand after the Symposium to the HeronIsland, Lizard Island and Orpheus IslandResearch Stations. Exciting and culturallysignificant Australian social events andthe Symposium banquet will provideadditional networking opportunities fordelegates to develop collaborations andpartnerships to increase internationalcapacity in coral reef research, educationand environmental management.ICRS 2012 will attract an extensiveinternational media contingent, and theARC Centre expects to host some 100journalists, whose stories will increaseawareness of coral reef science acrossthe world.In developing ICRS 2012, the ARCCentre has established an ExecutiveCommittee (chaired by the SymposiumConvenor, Terry Hughes), linked to subcommitteesresponsible for fundraising(led by David Yellowlees), and developingthe scientific program (chaired by TerryDone). Two other sub-committees foroverseeing the proceeding publicationsand for field trips will be established in2010. The committee membership, listedon the Symposium website, is global.We sincerely thank everyone who hasvolunteered their expertise and support.Our objective is for ICRS 2012 to becarbon-neutral, and we are activelypursuing innovative ways to reducecarbon emissions.Eliza GlassonConference Co-ordinatorARC Centre of Excellencefor Coral Reef StudiesJames Cook UniversityTownsville QLD 4811AustraliaPhone: +61 7 4781 4844Fax: +61 7 4781 3015Email: eliza.glasson@jcu.edu.au2009 annual report 47

“The ARC Centre, too, is highly ambitious... in its determinationto remain at the cutting edge of world science... and itscommitment to drive forward the national and internationalagenda on the sustainable use and management of coral reefs.”Her Excellency, Ms Penelope Wensley, the Governorof Queensland. Opening the ARC Centre’s annualsymposium, Securing Coral Reef Futures,Brisbane, August 2009.48ARC Centre of Excellence for Coral Reef Studies© Giles Winstanley / pelagicon.com

Symposium 2010© Giles Winstanley / pelagicon.comA highlight of the ARC Centre’s 2010calendar will be hosting an inter-academysymposium on coral reefs, at the ShineDome in Canberra on October 7-8 th .The Centre’s annual symposia arean important feature of our outreachactivities. 2010 will be a particularlyspecial event as we will be presentingthe conference in partnership withthe Australian Academy of Scienceand The Royal Society, which iscelebrating its 350 th anniversary. TheCanberra symposium will incorporatepresentations by members of bothnational academies and the ARC Centreof Excellence for Coral Reef Studies, tocelebrate the birth, development andemergence of coral reef sciences.The Royal Society has a long history ofinvolvement with research on the GreatBarrier Reef. In 1928 they sponsored C.M. Yonge to lead an expedition to theLowe Isles in northern Queensland. Thiswas the world’s first detailed scientificstudy of coral and coral reefs. Lessthan 100 years later, Australian coralreef science and reef management areamong the most developed in the world,and every year close to 200 internationalscientists travel to the Great Barrier Reefto pursue their research.2010 is also the International Year ofBiodiversity. It is therefore fitting that TheRoyal Society is taking the opportunityto recognize the special importance ofthe world’s coral reefs as part of its 350 thanniversary. Celebrations will comprisefour major events: the 2-day symposium,a public forum and an exhibition atthe National Museum of Australia inCanberra, and a Frontiers of Sciencemeeting to be held in Perth.The Public Forum will be held in theNational Museum of Australia onthe evening of 7 th October. It will behosted by a science celebrity, withresearchers presenting short talksto a general audience. The NationalMuseum of Australia will host aspecial commemorative exhibitionto coincide with the Public Forumand Symposium. The exhibition willfeature artifacts from The RoyalSociety’s collection from Captain JamesCook’s exploration of Australia, aswell as historic items of significanceto marine science from Australianmuseums and private collections.Following the Canberra events, a UK-Australia Frontiers of Science meetingsponsored by The Royal Society andthe Australian Academy of Science willbe held in Perth, from 13 th -19 th October.Future leaders in marine science willpresent the latest advances in their fields,learn from each other about researchdevelopments in other marine sciencedisciplines and explore opportunities forcollaboration. Early career researchersfrom the ARC Centre of Excellence,Australian Postdoctoral Fellows TracyAinsworth and Natalie Ban, have beenselected by the Australian Academyof Science to represent Australia onthe organising committee for thisinternational meeting.2009 annual report 49

National Benefit Case StudyCase Study 1: Improved protection for the Coral SeaThe Coral Sea is bounded to the southby the 24 th parallel, by New Caledonia,Vanuatu and the Solomon Islands to theeast, Papua New Guinea and SolomonIslands to the north, and Queensland tothe west. It has a very rich biodiversityand is one of the few places remainingon Earth where large pelagic fishes(tuna, billfish and sharks) have not yetbeen severely depleted. Importantly, italso provides a refuge for some criticallyendangered species including theHawksbill and Green turtles. It thereforeconstitutes an extremely valuableresource with outstanding conservationvalues. Consequently, the ARC Centreof Excellence for Coral Reef Studiessupports the establishment of the CoralSea as one of the world’s largest marineprotected areas.Researchers in the ARC Centrehave recommended to the FederalGovernment that the whole Coral Seashould become a no-fishing area toprotect its immense environmentaland heritage values from escalatingoverfishing and climate change. Thereis overwhelming evidence, generatedby the ARC Centre and elsewhere, thatthe world’s marine ecosystems havebeen seriously degraded by overfishing,pollution and global warming. Elevenpercent of land habitats have beendesignated as parks to conserve theirbiodiversity and the ecosystem servicesthey provide to people. In contrast, lessthan 0.1 per cent of the world’s oceansare fully protected.In a media interview published worldwidein 2009, ARC Centre researcherJohn Pandolfi stated that “Fishingactivities in the Coral Sea contribute tosignificant declines of sharks, turtlesand seabirds. A single large no-takezone is the best approach for protectingthese pelagic and migratory speciesbecause they cannot be protectedinside small reserves.” The practicalityof this statement was confirmed byeconomic research undertaken bymembers of the Centre’s Program6 on Conservation Planning (p.26).Consideration of management costsis important for several reasons. First,resources must be available for effective,long-term management to ensureeffective conservation. Second, costs ofmanagement can be considerable, andshould therefore be explicitly addressedin the site design and selectionprocess. Third, current managementbudgets are rarely sufficient to achieveall their objectives. Incorporatingmanagement costs from the outsetof any planning exercise is critical.In collaboration with QueenslandNational Parks and Wildlife Service, BobPressey, Vanessa Adams and Natalie Banaddressed a key question that had notbeen considered – here or elsewhere– of whether there was a significantdifference in the estimated managementcost for different zoning proposals forthe Coral Sea. Specifically, what isthe difference in management costsbetween multiple use zones versus asingle large no-take area?The Centre’s researchers developedtwo novel approaches for estimatingthe management costs for a Coral SeaMarine Protected Area (MPA). Theyfirst examined the current operationalbudgets for existing CommonwealthMPAs to identify key indicators ofmanagement costs. The secondapproach identified managementrequirements for the Coral Sea, andestimated costs for these activities basedon expert interviews and on the existingoperating costs for the Great Barrier ReefMarine Park. The resulting managementestimates for the Coral Sea indicatethat a single large marine reserve is lessexpensive to manage than multiple-useareas of equivalent size with a 30%no-take component. Regardless of themethod used, the difference betweenthe costs of a 30% versus 100% notakescenarios is the same: it is about1.6 times more expensive to managea multiple-use area than the same areawith 100% protection.In May 2009, the Coral Sea was declaredas a Conservation Zone by the Hon.Peter Garrett, the Federal Minister forthe Environment, Heritage and the Arts.The new Conservation Zone constitutes972,000 km 2 of Australian waters andseabed from directly east of the GreatBarrier Reef Marine Park out to the edgeof Australia’s Exclusive Economic Zone.Minister Garrett said that “The CoralSea Conservation Zone will protect thisenvironmentally significant area fromincreasing pressures while the nationalmarine bioregional planning process isundertaken, with a final plan scheduledfor completion in 2010”.50ARC Centre of Excellence for Coral Reef Studies

4000 mSample publications:Almany, G, Connolly, S, Heath, D,Hogan, J, Jones, G, McCook, L,Mills, M, Pressey, R and Williamson,D (2009). Connectivity, biodiversityconservation and the design ofmarine reserve networks for coralreefs. Coral Reefs 28(2): 339-351.Calvo, E, Marshall, JF, Pelejero, C,McCulloch, MT, Gagan, MK andLough, JM (2007). Interdecadalclimate variability in the Coral Seasince 1708 A.D. Palaeogeography,Palaeoclimatology, Palaeoecology248(1-2): 190-201Game, ET, Grantham, HS, Hobday, AJ,Pressey, RL, Lombard, AT, Beckley,LE, Gjerde, K, Bustamante, R,Possingham, HP and Richardson,AJ (2009). Pelagic protected areas:The missing dimension in oceanconservation. Trends in Ecology &Evolution 24(7): 360-369.Hughes, TP (2009). Seascape patternsand dynamics of coral reefs. pp482-487. In The Princeton Guide toEcology. S. A. Levin (Ed.). PrincetonPress, Princeton.P A P U A N E W G U I N E APort MoresbyNew GuineaTorres StraitBamagaC a p eCape GrenvilleYo r k LockartRiverPe n i n s u l aEasternFieldsAshmore ReefCooktown2000 mCape MelvillePort Douglas3000 mA U S T R A L I AQ U E E N S L A N DSquare kilometre figure is approximate.0 kilometres0 nautical milesDAVID E. CHANDLER145° 151°154°157° 160°163°166°169°9°Cairns200400C oTownsville4000 mOsprey Reef2000 m3000 mBougainvilleReefFloraReefMooreReefs2000 m1000 m3000 m4000 m4000 m1000 m4000 m3000 m2000 m1000 mTagulaWillisHolmes Reefs Islets NATURE RESERVEMagdelaine CaysHerald Coringa IsletsCaysLihou ReefsFlinders ReefsTregrosse ReefsAbington ReefGREAT BARRIERREEFMackayr aCORINGA-HERALDNATIONALMARINE PARKRockhamptonGladstoneLIHOU REEFNATIONALNATURE RESERVEBundabergSwainReefsMaryboroughMarion Reef4000 m4000 mFraserIslandRossel3000 m3000 m3000 m3000 m4000 mSaumarez ReefsBird IsletWest IsletWreck ReefsSandy CapeFrederick ReefsCato I.4000 m2000 m2000 mProposed AustralianCoral Sea Heritage Park~1,000,000 square kilometreslMellish ReefExclusiveEconomicZone2000 m1000 mGuadalcanal4000 m3000 mS eSOLOMONISLANDSRennell4000 mÎles Chesterfield2000 m4000 m4000 m3000 m1000 m1000 m2000 mSan Cristobal1000 m7000 m7000 m3000 m6000 m6000 m3000 m4000 m3000 m5000 m5000 m4000 mS O U T HP A C I F I CO C E A NaNupaniNendeUtupua3000 m4000 m2000 m7000 m6000 m8000 m3000 m2000 mNewCaledoniaFranceNouméa2000 m1000 m2000 m7000 m8000 m4000 m3000 mTorres IslandsVanua LavaSanta MariaEspirituSantoMalakulaSanta CruzIslandsVanikoro Is.BanksIslands6000 m5000 m6000 m5000 m3000 m3000 m2000 mVANUATUPort-VilaÉfatéErromangoTannaOuvéaLifouMaré2000 m4000 mN O R T HP A C I F I CO C E A NP A P U ANEW GUINEAAREAC o r a l ENLARGEDS e a ABOVES O U T HP A C I F I CAUSTRALIAO C E A NNEWZEALANDANTARCTICAMap reproduced with thanks to the Pew FoundationEQUATOR1000 m12°15°18°21°24°2009 annual report 51

Media ReleasePhoto by Simon FoaleScientists call for ‘ocean parks’ to protect seasAn international team of scientists has called for thecreation of marine protected areas in the open oceans toprotect the world’s sea life from growing damage and losscaused by overexploitation, pollution and other humanimpacts.“Pelagic ecosystems now face a multitude of threatsincluding overfishing, pollution, climate change,eutrophication, mining and species introductions,” theresearchers warn in the journal Trends in Ecology andEvolution (TREE). These threats can act together to causefar greater damage to marine food chains, fish stocks andecosystems.“Mobile pelagic species also suffer from the cumulativeimpact of sublethal stressors. Chronic exposure to chemicaland acoustic pollution from shipping, military activitiesor oil and gas exploration and exploitation can lead toimmunosuppression and reproductive failure in marinemammals,” they add.The high seas provide almost 80 per cent of humanity’sfish supplies, carry out half the photosynthesis (conversionof solar energy to sustain life) that takes place on the planetand, through their ability to absorb CO 2, are a dominantinfluence over the speed and extent of climate change.“It is clear from declines in many species that thereis inadequate protection for pelagic biodiversity andecosystems,” the researchers from Australia, South Africaand Poland say.“Fewer protected areas exist in the open ocean than inany other major ecosystem on Earth,” explains ProfessorBob Pressey of the ARC Centre of Excellence for CoralReef Studies, a co-author of the article.“Although there is growing support for the idea ofmarine protected areas in the open oceans, critics haveargued they would be difficult and costly to enforce andmanage in the ever-changing ocean environment.“However my colleagues and I consider that recentadvances in conservation science, oceanography andfisheries science can provide the necessary evidence, toolsand information to operate these ‘ocean parks’ for theconservation of marine species that live in the high seas.The scientists argue ocean protected areas should beseen as simply another form of marine protected area,except that they will extend in three dimensions – acrossthe surface and deep into the water itself.They note that on the high seas, there is no single globalbody with the authority to establish protected areas or toregulate access to and use of an area for more than onepurpose. However they say progress can be made throughRegional Fisheries Management Organizations, theInternational Maritime Organisation and by individualcountries doing more to protect the outer parts of their 200mile sovereign territories.By reducing the cumulative impact of human activitieson the world’s oceans, MPAs can help to mitigate theseverity of particular threats that cannot be directlycontrolled: “We believe that pelagic MPAs have now comeof age as an important tool in the planet’s last frontier ofconservation management.”Game, ET, Grantham, HS, Hobday, AJ, Pressey, RL,Lombard, AT, Beckley, LE, Gjerde, K, Bustamante, R,Possingham, HP and Richardson, AJ (2009). Pelagicprotected areas: The missing dimension in oceanconservation. Trends in Ecology & Evolution 24(7):360-369.19 October 200952ARC Centre of Excellence for Coral Reef Studies

A new ISI Web of Science analysis of journal publicationsand citations identifies the ARC Centre of Excellence forCoral Reef Studies as the premier climate change researchinstitution in Australia, with three Centre researchers rankedamong the top 20 researchers in the world for total numberof citations on climate change papers.www.sciencewatch.com/ana/fea/pdf/09novdecFea.pdf© Giles Winstanley / pelagicon.com2009 annual report 53

National Benefit Case StudyCase Study 2: Informing governments on responding to Climate ChangeThe 2009 United Nations climate changesummit in Copenhagen attracted >100world leaders, including the PrimeMinister of Australia. The ecological,social and economic consequencesof climate change for coral reefs inAustralia and throughout the tropics arecritical issues that pervade all of the ARCCentre’s research programs. The GreatBarrier Reef alone contributes $5.4 billionannually to the Australian economy – $5.1billion from the tourism industry; $153million from recreational activity; and$139 million from commercial fishing.The ARC Centre of Excellence for CoralReef Studies is a global leader in climatechange research, producing so far wellover 500 papers since 2005 on thisbroad inter-disciplinary topic. In 2009, ISIWeb of Science analysed 28,000 journalarticles on climate change researchpublished world-wide over the pastdecade. From this vast data-set, Webof Science-Science Watch identifiedthe most-cited institutions and authorsglobally. Among the leading institutions,James Cook University – headquartersof the ARC Centre of Excellence forCoral Reef Science - is ranked 2nd inthe world in terms of impact, measuredas citations per paper in climate changeresearch. Among the top papers of thedecade, the most highly-cited climatechangepublication led by an Australianauthor is a 2003 Science paper by CentreDirector, Terry Hughes and colleagues,entitled “Climate Change, HumanImpacts, and the Resilience of CoralReefs”. According to Web of Science,three Australians rank among the top 20researchers in the world for the numberof citations their climate change papershave received - ARC Centre membersOve Hoegh-Guldberg, Terry Hughes andJohn Pandolfi.The ARC Centre engages with manyend-users of climate change research,in Australia and globally. For example,Australian Academy of Science FellowsMalcolm McCulloch and Terry Hughesjoined colleagues from Brazil, Canada,China, Germany, New Zealand, Mexico,Japan, and Sweden in 2009 to producean Inter-Academy statement on oceanacidification. The statement, timed inadvance of the Copenhagen UnitedNations Framework Convention onClimate Change (UNFCCC) negotiations,summarizes the current state of thescience, and is aimed at policy-makers.In September, Deputy Director, OveHoegh-Guldberg provided Congressionalbriefings on climate change and oceanacidification, in Washington DC. InOctober, the ARC Centre’s Directorprovided a plenary talk on climatechange, adaptation and coral reefs, at the2009 ASEAN Conference on Biodiversityin Singapore, preceding the ASEANMinisterial Meeting on the Environment.In Australia, the Federal and Queenslandenvironment ministers acknowledgedthe key research provider role of theARC Centre, the Australian Institute ofMarine Science, and the CommonwealthScientific and Industrial ResearchOrganization, in their formal responseto the 2009 Great Barrier Reef OutlookReport. The report is a legislativerequirement, presented every 5 yearsto both Houses of the AustralianParliament. The inaugural 2009 reportprovides a summary of many of theARC Centre’s research findings, andwill inform policy and managementdecisions. In Western Australia, DeputyDirector Malcolm McCulloch provideda series of briefings to the WesternAustralian Department of Environmentand Conservation. In November, theCentre was a major contributor to abriefing on emission reduction targetsand the Great Barrier Reef, provided toAustralian Members of Parliament andSenators, in Parliament House, Canberra.The ARC Centre’s Director and twoDeputy Directors, along with PartnerInvestigator, Janice Lough from theAustralian Institute of Marine Science,contributed to the briefing, under theauspices of the Federation of AustralianScientific and Technological Societies.The ARC Centre contributed seniorpersonnel to the team that drafted theNational Climate Change AdaptationResearch Plan for Marine Biodiversityand Resources. Subject to Ministerialapproval, the national plan provides aframework to guide research fundingdecisions, and identifies the researchrequired over the next 5-7 years to informpolicy development and management ofmarine resources. The plan focuses onaquaculture, commercial and recreationalfisheries, conservation, and tourism.Sample 2009 publications:Brierley, AS and Kingsford, MJ (2009).Impacts of climate change on marineorganisms and ecosystems. CurrentBiology 19: 602-614.Cinner, JE, McClanahan, TR, Graham,NAJ, Pratchett, MS, Wilson, SKand Raina, J-B (2009). Gear-basedfisheries management as a potentialadaptive response to climate changeand coral mortality. Journal of AppliedEcology 46: 724-732.de Freitas, DM, Kininmonth, S andWoodley, S (2009). Linking scienceand management in the adoption ofsensor network technology in theGreat Barrier Reef coast, Australia.Computers, Environment and UrbanSystems 33(2): 111-121.McCook, L, Almany, G, Berumen, M,Day, J, Green, A, Jones, G, Leis,J, Planes, S, Russ, G, Sale, P andThorrold, S (2009). Managementunder uncertainty: Guide-lines forincorporating connectivity into theprotection of coral reefs. Coral Reefs28(2): 353-366Rockstrom, J, and 28 co-authors (2009).A safe operating space for humanity.Nature 461: 472-475.54ARC Centre of Excellence for Coral Reef Studies

Photo by Simon FoaleMedia ReleaseNemo “won’t be coming home”Nemo, the lovable clownfish of movie fame, may beunable to find his way home as the world’s oceans acidifydue to human-derived carbon emissions.Fish lose the sense of smell that guides them homewhen sea water becomes more acidic – with potentiallydevastating consequences for sea life, an internationalteam of scientists has discovered.Like many reef and coastal fish, Nemos are swept offtheir home reef into the open ocean as tiny babies and usetheir acute sense of smell to find their way back again.The researchers tested clownfish raised in normal andslightly more acidic seawater to see what effect it had ontheir sense of smell. To their dismay they found that thefish, normally acutely sensitive to different smells in thewater, became confused when the water they were raisedin was more acidic than usual.“This is a disturbing finding, because the tiny larvae ofmany coastal fish probably rely on scent cues in the waterto help locate adult habitat. Any disruption to their abilityto navigate could have far-reaching implications for thefuture of these fish populations.” says lead author ProfPhilip Munday of the ARC Centre of Excellence for CoralReef Studies.Ocean acidification, caused by the absorption of humanreleasedcarbon dioxide (CO 2) at the ocean surface, isnow recognized as a serious threat to marine ecosystems,the researchers from James Cook, Moscow and Oslouniversities say.“Global ocean pH is estimated to have dropped by0.1 units since preindustrial times and is projected to fallanother 0.3-0.4 units by 2100 due to current and futureCO 2emissions.”“Orange clownfish – or nemos - mostly live on oceanicreefs surrounding vegetated islands and research hasshown that baby fish can discriminate between seawaterfrom reefs surrounding vegetated islands versus seawaterfrom reefs without islands. This is what enables many ofthe baby clownfish to find their way back to the reef wherethey were hatched”, says co-author Geoff Jones.In normal sea water nemos are strongly attracted toscents from anemones on their home reefs and tropicalrainforest trees on nearby land – but avoid the smell ofswamp trees or tropical grasses.Nemos reared in slightly more acidic water wereattracted to a range of environmental smells, includingthose they normally avoided and that indicated a habitatless suited to their needs. Nemos reared in seawater at pH7.6 showed no response to scent cues at all.“Our results show for the first time that elevated CO 2and reduced seawater pH can affect the behaviouraldecisions of marine organisms during critical stagesof their life-history. In this case, acidification disruptedthe olfactory mechanism by which clownfish larvaediscriminate between cues that may be useful for locatingsuitable adult habitat and other cues that could lead larvaeto unsuitable settlement sites.“Disruption to this process would have significantconsequences for the replenishment of adult populationsand could lead to declines of many coastal species,” theyconclude.Munday, PL, Dixson, DL, Donelson, JM, Jones, GP,Pratchett, MS, Devitsina, GV and Daving, KB (2009).Ocean acidification impairs olfactory discriminationand homing ability of a marine fish. Proceedings of theNational Academy of Sciences 106(6): 1848-1852.4 February 20092009 annual report 55

publicationsThe ARC Centre of Excellence for CoralReef Studies produced 224 publicationsin 2009, continuing the rapid growth inoutput exhibited since 2004. Accordingto ISI Web of Science, the ARC Centreremains the first-ranked institutionglobally for both the number of journalpublications and citations in coral reefscience. The average Impact Factor forall 203 journal articles published in 2009was 4.2.Fifty-three of the 2009 articles arein journals with Impact Factorsgreater than four, including top-tierjournals such as Science, Nature,PNAS and Current Biology. Number of publications by membersof the ARC Centre of Excellencefor 2004-2009Number of publications2502001501005002004200520062007Year20082009The Centre’s research outputs werepublished in a total of 90 journals,spanning many fields of research.For example, the titles of thesejournals refer to each of the followingdisciplines: archaeology, biochemistry,botany, conservation biology, ecology,evolution, fisheries, immunology,modelling, oceanography, paleobiology,petrology, photobiology, physiology,genomics, geochemistry, social science,systematics, and many more.Citations of the Centre’s publicationscontinue to grow, increasing nearly 5-foldsince 2004. Twenty-five researcherswere each cited >200 times in 2009,nine of the Centre members had >500citations, and three had >1000 citationsin the 12-month reporting period. Summed citations to members ofthe ARC Centre of Excellence eachyear for 2004-2009Number of citations16000140001200010000800060004000200002004200520062007YearLeague table achievementsin 2009 include:20082009• Three Program Leaders in theCentre are recognized by ISI asHighly Cited Researchers in EarthSciences (Malcolm McCulloch)and Ecology/Environment (TerryHughes and Bob Pressey).• The Faculty of 1000 Biologyhighlighted six of the ARC Centre’spublications for review in 2009.• ISI Essential Science Indicatorsidentified two of the Centre’srecent articles as Hot Papers, whichreceived an unusually high number ofcitations within 2 years of publication:• Hoegh-Guldberg, O, Mumby,PJ, Hooten, AJ, Steneck, RS,Greenfield, P, Gomez, E, Harvell,CD, Sale, PF, Edwards, AJ,• Caldeira, K, Knowlton, N, Eakin,CM, Iglesias-Prieto, R, Muthiga,N, Bradbury, RH, Dubi, A andHatziolos, ME (2007). Coral ReefsUnder Rapid Climate Change andOcean Acidification. Science 318:1737-1742.• Pratchett MS, Munday PL,Wilson SK, Graham NAJ, CinnerJE, Bellwood DR, Jones GP,Polunin NVC, McClanahan TR(2008) Effects of climate-inducedcoral bleaching on coral-reeffishes - ecological and economicconsequences. Oceanographyand Marine Biology: An AnnualReview 46:251-296ISI Essential Science Indicatorsidentified four Research Fronts in2009 that highlight the Centre’sresearch. A research front is a groupof highly cited papers, referred toas core papers, in an emergingtopic defined by a cluster analysis.Seventeen core papers in theseResearch Fronts including 7 inScience, Nature and PNAS, were coauthoredby G. Almany, D. Bellwood,C. Folke, N. Graham, O. Hoegh-Guldberg, T. Hughes, G. Jones, M.Kingsford, M. McCormick, S. Planes,M. Pratchett, B. Pressey, R. Steneck,S. Wilson, and D. Yellowlees.56ARC Centre of Excellence for Coral Reef Studies

publications listBooks[1] van Oppen, MJH and Lough,JM (2009). Coral bleaching:patterns, processes, causesand consequences 178pp.Springer, Berlin Heidelberg.Book Sections[2] Cinner, JE, McClanahan, TR,Abunge, C and Wamukota,AW (2009). Humandimensions of conservingKenya’s coral reefs. InAdvances in coastal ecology:People, processes andecosystems in Kenya. J.Hoorweg and N. A. Muthiga(Eds.). African Studies Centre,Leiden, Netherlands.[3] Connolly, SR (2009).Macroecological theoryand the analysis of speciesrichness gradients. pp279-309. In Marine Macroecology.J. D. Witman and K. Roy(Eds.). The University ofChicago Press, Chicago.[4] Eakin, CM, Lough, JM andHeron, SF (2009). Climatevariability and change:monitoring data and evidencefor increased coral bleachingstress. pp41-67. In CoralBleaching. M. J. H. vanOppen and J. M. Lough(Eds.). Springer, BerlinHeidelberg.[5] Ferguson, KH (2009). That’snot a reef, now that’s a reef:a century of (re)placing theGreat Barrier Reef. pp223-236. In ECOSEE: Image,Rhetoric, and Nature. S. I.Dobrin and S. Morey (Eds.).State University of New YorkPress, New York.[6] Hughes, TP (2009).Confronting the global declineof coral reefs. pp140-166. InLoss of Coastal Ecosystems.C. Duarte (Ed.). BBVAFoundation, Madrid.[7] Hughes, TP (2009). Seascapepatterns and dynamics ofcoral reefs. pp482-487. In ThePrinceton Guide to Ecology.S. A. Levin (Ed.). PrincetonPress, Princeton.[8] Lough, JM and van Oppen,MJH (2009). Introduction:coral bleaching - patterns,processes, causes andconsequences. pp1-5. InCoral Bleaching. M. J. H.van Oppen and J. M. Lough(Eds.). Springer, BerlinHeidelberg.[9] McClanahan, TR, Weil, E,Cortés, J, Baird, AH andAteweberhan, M (2009).Consequences of coralbleaching for sessile reeforganisms. pp121-138. InCoral Bleaching. M. J. H.van Oppen and J. M. Lough(Eds.). Springer, BerlinHeidelberg.[10] Pratchett, MS, Wilson, SK,Graham, NAJ, Munday,PL, Jones, GP and Polunin,NVC (2009). Coral bleachingand consequences formotile reef organisms:past, present and uncertainfuture effects. pp139-158.In Coral Bleaching. M. J.H. van Oppen and J. M.Lough (Eds.). Springer, BerlinHeidelberg.[11] Pressey, RL, Watts, ME,Barrett, TW and Ridges,MJ (2009). The C-Planconservation planningsystem: origins, applications,and possible futures.pp211-234. In Spatialconservation prioritization:Quantitative methods andcomputational tools. A.Moilanen, K. A. Wilson andH. P. Possingham (Eds.).Oxford University Press,Oxford, UK.[12] Souza Junior, WC andFidelman, PIJ (2009). TheTechnopolitics of waterin Brazil. pp195-211. InGovernança da água noBrasil. W. C. Ribeiro (Ed.).Annablumme Press, Brazil.[13] Turner, WR and Pressey,RL (2009). Building andimplementing systems ofconservation areas. pp538-547. In The Princeton guideto ecology. S. Levin (Ed.).Princeton University Press,Princeton.[14] van Oppen, MJH, Baker,AC, Coffroth, MA andWillis, BL (2009). Bleachingresistance and the role ofalgal endosymbionts. pp83-102. In Coral Bleaching. M.J. H. van Oppen and J. M.Lough (Eds.). Springer, BerlinHeidelberg.[15] van Oppen, MJH and Lough,JM (2009). Synthesis:Coral bleaching - patterns,processes, causes andconsequences. pp175-176.In Coral Bleaching. M. J.H. van Oppen and J. M.Lough (Eds.). Springer, BerlinHeidelberg.Journal Articles[16] Abrego, D, van Oppen,MJH and Willis, BL (2009).Highly infectious symbiontdominates initial uptake incoral juveniles. MolecularEcology 18(16): 3518-3531.[17] Abrego, D, van Oppen,MJH and Willis, BL (2009).Onset of algal endosymbiontspecificity varies amongclosely related species ofAcropora corals during earlyontogeny. Molecular Ecology18(16): 3532-3543.[18] Adjeroud, M, Michonneau,F, Edmunds, P, Chancerelle,Y, de Loma, T, Penin, L,Thibaut, L, Vidal-Dupiol,J, Salvat, B and Galzin,R (2009). Recurrentdisturbances, recoverytrajectories, and resilienceof coral assemblages on asouth central Pacific reef.Coral Reefs 28(3): 775-780.[19] Ainsworth, TD and Hoegh-Guldberg, O (2009). Bacterialcommunities closelyassociated with coral tissuesvary under experimentaland natural reef conditionsand thermal stress. AquaticBiology 4(3): 289-296.[20] Almany, G, Connolly, S,Heath, D, Hogan, J, Jones,G, McCook, L, Mills, M,Pressey, R and Williamson,D (2009). 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Otolith chemistryof the non-dispersingreef fish Acanthochromispolyacanthus: cross-shelfpatterns from the centralGreat Barrier Reef. MarineEcology-Progress Series377: 279-288.[131] Kitahara, MV and Cairns,SD (2009). A revision ofthe genus DeltocyathusMilne Edwards & Haime,1848 (Scleractinia,Caryophylliidae) fromNew Caledonia, withthe description of a newspecies. Zoosystema 31(2):233-248.[132] Kool, JT (2009). An objectoriented,individual-basedapproach for simulatingthe dynamics of genes insubdivided populations.Ecological Informatics 4(3):136-146.[133] Krajewski, JP, Bonaldo, RM,Sazima, C and Sazima, I(2009). Octopus mimickingits follower reef fish.Journal of Natural History43(3-4): 185-190.60ARC Centre of Excellence for Coral Reef Studies

[134] Kroon, FJ, Munday,PL and Westcott, DA(2009). Equivalent wholebodyconcentrations of11-ketotestosterone infemale and male coral gobyGobiodon erythrospilus, abidirectional sex-changingfish. Journal of Fish Biology75(3): 685-692.[135] Kvennefors, E and Roff,G (2009). Evidenceof cyanobacteria-likeendosymbionts in Acroporidcorals from the GreatBarrier Reef. Coral Reefs28(2): 547.[136] Lemberget, T, McCormick,M and Wilson, D (2009).Environmental influenceson the replenishmentof lizardfish (familySynodontidae) in CaribbeanPanama. Coral Reefs 28(3):737-750.[137] Lemberget, T andMcCormick, MI (2009).Replenishment successlinked to fluctuatingasymmetry in larval fish.Oecologia 159(1): 83-93.[138] Leray, M, Beldade, R,Holbrook, SJ, Schmitt, RJ,Planes, S and Bernardi,G (2009). 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Marine Ecology-Progress Series 392: 81-92.[151] Mieog, JC, Olsen, JL,Berkelmans, R, Bleuler-Martinez, SA, Willis, BL andvan Oppen, MJH (2009).The roles and interactionsof symbiont, host andenvironment in definingcoral fitness. PLoS ONE4(7): e6364.[152] Mieog, JC, Van Oppen,MJH, Berkelmans, R,Stam, WT and Olsen,JL (2009). Quantificationof algal endosymbionts(Symbiodinium) in coraltissue using real-timePCR. Molecular EcologyResources 9(1): 74-82.[153] Miller, D and Ball, E (2009).The gene complement ofthe ancestral bilaterian -was Urbilateria a monster?Journal of Biology 8(10): 89.[154] Montagna, P, McCulloch,M, Taviani, M, Trotter, J,Silenzi, S and Mazzoli,C (2009). An improvedsampling method forcoral P/Ca as a nutrientproxy. 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MarineEcology-Progress Series388: 235-242.[159] Munday, PL, Dixson, DL,Donelson, JM, Jones, GP,Pratchett, MS, Devitsina,GV and Daving, KB (2009).Ocean acidification impairsolfactory discriminationand homing ability of amarine fish. Proceedingsof the National Academyof Sciences 106(6): 1848-1852.[160] Munday, PL, Donelson, JM,Dixson, DL and Endo, GGK(2009). Effects of oceanacidification on the early lifehistory of a tropical marinefish. Proceedings of theRoyal Society B-BiologicalSciences 276(1671): 3275-3283.[161] Nagelkerken, I, van derVelde, G, Wartenbergh, SLJ,Nugues, MM and Pratchett,MS (2009). Cryptic dietarycomponents reducedietary overlap amongsympatric butterflyfishes(Chaetodontidae). Journalof Fish Biology 75(6): 1123-1143.[162] Nayar, S, Collings, GJ,Miller, DJ, Bryars, S andCheshire, AC (2009).Uptake and resourceallocation of inorganiccarbon by the temperateseagrasses Posidoniaand Amphibolis. Journalof Experimental MarineBiology and Ecology 373(2):87-95.[163] Nilsson, GE, Crawley, N,Lunde, IG and Munday,PL (2009). Elevatedtemperature reduces therespiratory scope of coralreef fishes. Global ChangeBiology 15(6): 1405-1412.[164] Noreen, AME, Harrison,PL and Van Oppen, MJH(2009). Genetic diversity andconnectivity in a broodingreef coral at the limit of itsdistribution. Proceedingsof the Royal SocietyB: Biological Sciences276(1675): 3927-3935.[165] Norstrom, AV, Nystrom,M, Lokrantz, J and Folke,C (2009). Alternative stateson coral reefs: beyond coralmacroalgalphase shifts.Marine Ecology-ProgressSeries 376: 295-306.[166] Ojeda-Martinez, C,Casalduero, FG, Bayle-Sempere, JT, Cebrian, CB,Valle, C, Sanchez-Lizaso, JL,Forcada, A, Sanchez-Jerez,P, Martin-Sosa, P, Falcon,JM, Salas, F, Graziano, M,Chemello, R, Stobart, B,Cartagena, P, Perez-Ruzafa,A, Vandeperre, F, Rochel,E, Planes, S and Brito,A (2009). A conceptualframework for the integralmanagement of marineprotected areas. Ocean &Coastal Management 52(2):89-101.2009 annual report 61

[167] Olson, ND, Ainsworth, TD,Gates, RD and Takabayashi,M (2009). Diazotrophicbacteria associated withHawaiian Montipora corals:diversity and abundance incorrelation with symbioticdinoflagellates. Journalof Experimental MarineBiology and Ecology 371(2):140-146.[168] Ortiz, J, Gomez-Cabrera,M and Hoegh-Guldberg, O(2009). Effect of colony sizeand surrounding substrateon corals experiencinga mild bleaching eventon Heron Island reef flat(southern Great BarrierReef, Australia). Coral Reefs28(4): 999-1003.[169] Page, CA, Baker, DM,Harvell, CD, Golbuu, Y,Raymundo, L, Neale, SJ,Rosell, KB, Rypien, KL,Andras, JP and Willis, BL(2009). Influence of marinereserves on coral diseaseprevalence. Diseases ofAquatic Organisms 87(1-2):135-150.[170] Pandolfi, JM (2009).Evolutionary impactsof fishing: overfishing’s‘Darwinian debt’. BiologyReports 1(43): 1-3.[171] Peplow, LM, Kingsford,MJ, Seymour, JE andvan Oppen, MJH (2009).Eight microsatellite loci forthe Irukandji syndromecausingcarybdeid jellyfish,Carukia barnesi (Cubozoa,Cnidaria). Molecular EcologyResources 9(2): 670-672.[172] Planes, S, Jones, GP andThorrold, SR (2009). Larvaldispersal connects fishpopulations in a networkof marine protected areas.Proceedings of the NationalAcademy of Sciences106(14): 5693-5697.[173] Planes, S, Lecchini, D,Romans, P and Mills, SC(2009). Effects of postsettlementmortality onsize and parasite load injuvenile Diplodus vulgarisand D. sargus in theMediterranean. AquaticBiology 6(1-3): 153-158.[174] Pratchett, MS, Schenk,TJ, Baine, M, Syms, Cand Baird, AH (2009).Selective coral mortalityassociated with outbreaksof Acanthaster planci L.in Bootless Bay, PapuaNew Guinea. MarineEnvironmental Research67(4-5): 230-236.[175] Pressey, RL and Bottrill,MC (2009). Approaches tolandscape and seascapescaleconservation planning:convergence, contrastsand challenges. Oryx 43(4):464-475.[176] Puill-Stephan, E, Willis,BL, van Herwerden, Land van Oppen, MJH(2009). Chimerism in wildadult populations of thebroadcast spawning coralAcropora millepora on theGreat Barrier Reef. PLoSONE 4(11).[177] Raina, J-B, Tapiolas, D,Willis, BL and Bourne, DG(2009). Coral-associatedbacteria and their role inthe biogeochemical cyclingof sulfur. Applied andEnvironmental Microbiology75(11): 3492-3501.[178] Raventos, N, Ferrari, Band Planes, S (2009).Differences in populationparameters and behaviourof the herbivorous fishSarpa salpa betweenprotected and unprotectedseagrass meadowsin the north-westernMediterranean. 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Coral-virus interactions:a double-edged sword?Symbiosis 47(1): 1-8.[201] Veron, JEN, Hoegh-Guldberg, O, Lenton, TM,Lough, JM, Obura, DO,Pearce-Kelly, P, Sheppard,CRC, Spalding, M, Stafford-Smith, MG and Rogers, AD(2009). The coral reef crisis:the critical importanceof

Recognition of Excellenceby Centre MembersThe scientific achievements of manymembers of the ARC Centre ofExcellence for Coral Reef Studies wererecognised during 2009 through awardsand peer-recognition. Examples include:• The Australian Academy of Sciencerecognised the achievementsof two of the Centre’s programleaders. Malcolm McCulloch wasawarded the Jaeger Medal forResearch in Earth Science for thecontribution throughout his careerto “the study of the solid earthand environmental issues”. SeanConnolly won the Fenner Medalfor Research in Biology. This isawarded for distinguished researchby an early career researcherunder the age of 40. Sean wasrecognised for his “researchon the processes influencingpopulation dynamics, ecologicalinteractions and biodiversity”.• Australian Postdoctoral Fellow,Natalie Ban, won the inauguralBommies Award of the Great BarrierReef Foundation along with herassociate Eddie Game from TheNature Conservancy. Her project isentitled “Conservation objectivesto minimize the impacts of climatechange on the Great Barrier Reef”.• The book The Great Barrier Reefedited by Ove Hoegh-Guldberg,Pat Hutchings and Mike Kingsfordwas awarded a CommendationCertificate for a Zoological Textat the 2009 Whitley Awardshosted by the Royal ZoologicalSociety of New South Wales.• Three of the Centre’s Fellows wereselected by the Australian Academyof Science for International ScienceLinkages – Science AcademiesProgram funding. John Pandolfi(UQ), Tracy Ainsworth (JCU), AndrewBaird (JCU) will visit the University ofCalifornia, University of Hawaii andAcademia Sinica respectively underthis scheme.• Professor Peter Mumby wasawarded one of the AustralianResearch Council’s inauguralLaureate Fellowships in late 2009.Peter’s move to Australia from theUniversity of Exeter in the United•Kingdom will allow him to forgenew collaborations across the ARCCentre’s nodes in Australia. Othersuccesses in latest ARC Fellowshiprounds include Glenn Almany,Andrew Baird (Future Fellowships),and Natalie Ban and Nick Graham(Australian Postdoctoral Fellowships).At James Cook University, severalof the Centre’s researchers wererecognised within the University:• Terry Hughes and Bob Presseywere appointed as DistinguishedProfessors in September. Thisnew title is bestowed on leadingresearchers who have achievedextraordinary levels in theirchosen fields.• Morgan Pratchett won the JCUSupervisor of the Year award inthe early career category.• Philip Munday, Morgan Pratchettand Nick Graham won the JCUVice-Chancellor Excellence Awardfor Research and Supervision.Courtesy of the Australian Academy of Science © Irene DowdyProfessor Sean Connollywas awarded the FennerMedal for Research inBiology by the AustralianAcademy of Science64ARC Centre of Excellence for Coral Reef Studies

Courtesy of the Australian Academy of Science © Irene DowdyProfessor Malcolm McCulloch was awarded theJaeger Medal for Research in Earth Science by theAustralian Academy of Science2009 annual report 65

Performance MeasuresResearch findingsMeasure Target 2009 Outcome 2009Number of publications (p.56) 145 224Publications in journals with an impact factor > 4 38 53Number of citations (p.56) 6500 14194Invitations to provide plenary addresses at internationalconferences30 43Invitations to provide review articles 35 42Number and nature of commentaries about the Centre’sachievements850 2190Awards, prizes or recognition (p.64) 17 26Research training and professional educationMeasure Target 2009 Outcome 2009Number of postgraduates enrolled (p.34) 120 over 5 years 159 enrolled in 2009Number of postgraduate completions 70 over 5 years 25Number of Honours students 60 over 5 years 15 enrolled in 2009Number of professional workshops 14 18Participation in professional workshops 20 37Number and level of graduate student courses andworkshops in the priority area(s)10 1666ARC Centre of Excellence for Coral Reef Studies

International, national and regional links and networksMeasure Target 2009 Outcome 2009Number of international visitors 65 79Number of national and international Working Groups 1645 researcher participationsin 20 working groupsNumber of visits to overseas laboratories and researchfacilitiesMembership of national and international boards and advisorycommittees50 5840 57Number of cross-institutional publications 95 161Number of multi-institutional supervisory arrangements ofgraduate students50 57Commercialisation:Number of internationally funded studentsNumber of consultancies and contract research20 over 5 years55723Number of government, industry and business briefings 30 82Number of Centre trained/ing personnel in knowledge /technology transfer and commercialization5 5Public awareness programs:Website hitsPublic awareness presentations1.5 million124.5 million45Organisational supportMeasure Target 2009 Outcome 2009Annual cash contributions from Collaborating Organisations $1.36m $2.2mAnnual in-kind contributions from Collaborating Organisations $3.2m $5.7mNumber of new Organisations recruited to or involved in the Centre 5 5Level and quality of infrastructure provided to the Centre $1.07m $1.1mAnnual cash contributions from other organisations $0.26m $2.3m2009 annual report 67

Performance MeasuresGovernanceMeasure Target 2009 Outcome 2009Breadth and experience of the membersof the Advisory BoardFrequency and effectiveness of AdvisoryBoard meetingsQuality of the Centre strategic planSenior representation from all nodes.Representation of eminent internationalresearchers. Members with commercialand business links2 Centre Advisory Board meetings p.a.4 Scientific Management Committeemeetings p.a.The Centre’s progress againstthe plan will be formally reportedto the Advisory Board and berenewed in light of outcomesSee page 7See page 7Strategic Plan reviewed andendorsed by the Centre AdvisoryBoard. Ongoing performanceagainst plan reviewed at ScientificManagement Committee meetingsEffectiveness of arrangements to manageCentre nodes1.2.Meetings of the ScientificManagement Committee whereeach node and program isrepresentedMonthly nodal leader phone or videoconferences1.2.All nodes and research programsrepresented at ScientificManagement Committee meetingsRegular nodal and program leadermeetings held3.Annual rotational visits to the nodes3.There were 24 cross-nodal visitsin 2009. Additionally, memberstravelled to Brisbane for the Centre’sannual meeting and symposium.4.Annual research retreats for allCentre participants4.Research planning meetings wereheld by each research program5.Annual research program planningmeetings with cross-nodalattendance5.Cross-nodal attendance at allresearch planning meetings6.Number of co-supervisoryarrangements for students6.577.Number of multi-nodal seminar anddiscussion groups7.40The adequacy of the Centre’s KeyPerformance MeasuresInternational benchmarking toresearch in top internationalmarine research centres.The Centre is ranked #1 in the world forcitations and outputs in coral reef science68ARC Centre of Excellence for Coral Reef Studies

National BenefitMeasure Target 2009 Outcome 2009Measures of expansion ofAustralia’s capability in thepriority area(s)Case studies of economic,social, cultural orenvironmental benefits100% increase on 2004 benchmark by 201034 briefings to government, business andindustry groups17 cross-nodal publications90 cross-institutional publications2 to be highlighted in the annual report anddistributed to media agencies2.5 times the number of publications in the2004 benchmark4.8 times the number of citations in the 2004benchmark82 briefings30 cross-nodal publications161 cross-institutional publications39 Media ReleasesSee page 502009 annual report 69

Financial StatementARC Centre of Excellence for Coral Reef StudiesStatement of Operating Income and Expenditure for year ended 31 December 2009Income2008$2009$ARC Centre Grant $2,598,470 $2,651,090ARC Fellowships 789,965 932,744ARC Discovery 71,418ARC Linkages 150,000ARC Networks 30,000Host Institutions cash support 1,709,282 2,266,972Local GovernmentState Government 117,000 119,965Commonwealth Government other grants 356,000 408,423International and other contracts 297,900 571,923Total Income $5,868,617 $7,202,535ExpenditureSalaries 3,710,607 3,829,430Equipment 326,790 526,204Travel 1,144,558 1,236,948Research maintenance and consumables 1,133,984 1,087,630Scholarships 54,112 153,077Public outreach and administration 45,523 171,776Total Expenditure $6,415,573 $7,005,065Surplus (Deficit) $(546,956) $197,47070ARC Centre of Excellence for Coral Reef Studies

Financial StatusWith the announcement of the extension of the ARC Centre of Excellence to 2013 the operating cash and in-kind operating budgetfor the ARC Centre of Excellence for 2005-2013 currently totals $97m, more than triple the 2005 funding outlook. The chart belowindicates the budgeted level of income from the various funding sources.ARC Centre cash and inkind funding outlook 2005-2013 – Total funding $97mUWA $1m, 1%ANU $2m, 2%Industry partners & contracts $7m, 7%UQ $4m, 4% ARC CoE $23m, 24%JCU $42m, 44%ARC Fellowships $7m, 7%StateGovernment$3m, 3%CommonwealthGovernment / Other$5m, 5%ARC Other $3m, 3%2009 annual report 71

AcknowledgementsThe ARC Centre of Excellence for Coral Reef Studies thanks the following organisations and partners for their ongoing support:••••••••••••••••••••••••••American Australian AssociationAustralian Academy of ScienceAustralian Institute of Marine ScienceAustralian Coral Reef SocietyAustralian Geographical SocietyAustralian MuseumBeijer Institute for Ecological EconomicsCentre National de la Recherche ScientifiqueConservation InternationalDepartment of Environment, Water, Heritage and the ArtsEcological Society of AustraliaEnvironmental Futures NetworkEuropean CommissionGerman Federal Ministry for the Environment, NatureConservation and Nuclear SafetyGovernment of the Republic of IndonesiaGreat Barrier Reef FoundationGreat Barrier Reef Marine Park AuthorityGriffith UniversityHassall and Associates Pty LtdIan Potter FoundationIDP Education AustraliaLizard Island Research StationMacArthur FoundationMarine and Tropical Sciences Research FacilityNational Geographic SocietyNetwork in Genes and Environment in Development••••••••••••••••••••••••New Zealand Marsden FundPackard FoundationPADI FoundationProject AWARE FoundationQueensland Conservation CouncilQueensland Department of Premier and CabinetQueensland Department of Primary IndustriesQueensland Department of Employment, EconomicDevelopment & InnovationQueensland Parks & Wildlife ServiceResilience AllianceRoyal Swedish Academy of ScienceStockholm Resilience CentreThe Nature ConservancyUnited Nations UniversityUniversity of DelawareUniversity of MaineUniversity of PerpignanWestern Australian Department of CommerceWestern Australian Department of Environment andConservationWestern Indian Ocean Marine Science AssociationWildlife Conservation SocietyWildlife Preservation Society of AustraliaWorld Bank Global Environment Facility Coral Reef TargetedResearch ProgramWorld Wide Fund for NatureReport design and layout by Zephyrmedia (www.zephyrmedia.com.au)72ARC Centre of Excellence for Coral Reef Studies

ARC Centre of Excellence for Coral Reef StudiesJames Cook UniversityTownsvilleQueensland 4811AUSTRALIAPhone: +61 7 4781 4000Fax: +61 7 4781 6722Email: info@coralcoe.org.auwww.coralcoe.org.au