PhD Opportunities

Undertaking PhD studies at CoralCoE

The ARC Centre of Excellence for Coral Reef Studies is seeking applications from exceptional students to enroll in PhD studies under the supervision of leading researchers at its four nodes around Australia (James Cook University, the Australian National University, the University of Queensland and the University of Western Australia).

The scholarship cycle in Australia is on a calendar basis with closing dates for international applications at the end of August and domestic applications at the end of October; both with an expected starting date for successful applicants at the beginning of the following year. Suitable applicants will be required to go through a formal application at the relevant University and, if successful, will be awarded a scholarship and (at present) their tuition fees will be waived. Depending on the university and supervisor, there may be the possibility, in the case of outstanding applicants, for a top-up to their scholarship. To be competitive for a scholarship and fee waiver applicants must have a first class honours degree or Masters by research degree, preferably with a publication.

Many student applicants come with scholarships from another funding source such as granting agencies in their home country. We are happy to deal with these applications at any time of the year. Acceptance is dependent on the applicant meeting our academic criteria, has been accepted by a suitable supervisor and meets the language requirements.

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The following leading researchers in the Centre have expressed an interest in recruiting new exceptional postgraduate students. Their email addresses and areas of interest for research projects are listed. If you are interested, please contact one of the following to discuss opportunities. Please also copy all correspondence to the Chief Operations Officer Jenny Lappin (Jennifer.Lappin@jcu.edu.au) who oversees the process.

• Biochemistry, Molecular Biology and Bioinformatics
• Conservation Planning
• Coral Reef Ecology
• Coral Reef Oceanography
• Ecological Modelling
• Environmental Governance
• Human Dimensions and Social-Ecological Systems
• Coral Reef Ecology and Biology
• Ocean Acidification and Climate Change
• Reef Fish Ecology and Climate Change

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Biochemistry, Molecular Biology and Bioinformatics

Dr. Tracy Ainsworth

Email: tracy.ainsworth@jcu.edu.au

• Understanding the role of the fish gut microbiome under climate change
• Role of coral acclimation in recovery and regrowth after bleaching events
• Alterations populations and functional roles of the coral microbiome under climate change

Dr Sylvain Forêt
Email: sylvain.foret@anu.edu.au

• Comparative genomics of corals
• Genomic signature of adaptation to stress
• Dynamics of epigenomic regulations in corals, DNA methylation in particular
• Epigenetics and acclimatisation in corals
• Phylogenomics of corals and their relatives

Dr Sofia Fortunato
Email: sofia.valerofortunato@jcu.edu.au
Saving Nemo’s home project

• Signaling pathways involved on heat stress responses in sea anemones

Dr Hugo Harrison
Email: hugo.harrison@jcu.edu.au

• The role of hybridisation in the speciation of coral reef fishes
• Comparative genomics of fishes

Associate Professor Bill Leggat
Email: bill.leggat@jcu.edu.au

• Stress responses of Symbiodinium to climate change
• Development of metabolomic approaches as an early warning management tool for corals and seagrass
• The role of sea water temperature pulsing in coral acclimation

Professor David Miller
Email: david.miller@jcu.edu.au

• Molecular mechanisms of immunity and disease in corals
• Coral – microbe interactions, particularly mechanisms by which corals manipulate associated bacteria
• Developmental biology and metamorphosis in soft and hard corals
• The molecular mechanisms of calcification in corals, octocorals and calcareous sponges
• Comparative genomics of corals and other “lower” animals
• Stress responses and epigenetics of hard and soft corals

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Conservation Planning

Dr Michael Bode
Email: bodem@unimelb.edu.au

• Collaboration and competition between organisations in conservation landscapes
• Conservation finance: donors, features and actors

Professor Bob Pressey
Email: bob.pressey@jcu.edu.au

• Design of marine protected areas and use-zones within them
• Implementation requirements for turning conservation plans into conservation action: social, economic and political considerations
• Testing the effectiveness of marine habitats as surrogates for species distributions
• Planning to promote the persistence of ecological processes, including dispersal of larvae between reefs and patch dynamics of disturbance and resources
• Integrated conservation planning for coastal catchments and near-shore marine areas
• Improved ways of incorporating social and economic considerations into planning decisions
• Explaining and predicting reserve management costs from internal and external drivers
• Measuring the impact (difference made) by conservation reserves

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Coral Reef Ecology

Professor David Bellwood
Email: david.bellwood@jcu.edu.au

I am interested in the evolution and ecology of reef fishes.

• The global biogeography of coral reef species
• Developing new technologies for coral reef regeneration and recovery
• Understanding the importance of biodiversity on coral reefs
• Identifying critical ecosystem processes on coral reefs
• Evaluating the role of herbivorous fishes in reef systems
• Understanding direct human impacts and climate change on ecosystem processes
• Using fossils and phylogenies to unravel the evolution of reef fishes

Dr Andrew Hoey
Email: andrew.hoey1@jcu.edu.au

• Resilience and recovery of reef systems
• The role of macroalgae and ecological feedbacks in reef dynamics
• Anthropogenic and climate change effects on ecosystem function
• Biology, ecology and role of herbivorous fishes on coral reefs
• Effects of temperature on reef processes

Professor Peter Mumby
Email: p.j.mumby@uq.edu.au

• Coral reef resilience
• Marine reserve design
• Management of reef fisheries and their productivity
• Climate change impacts on ecosystem function
• Mapping ecosystem services
• Modelling coral reef futures with different management scenarios

Professor John Pandolfi
Email: j.pandolfi@uq.edu.au

• Effects of climate change on tropical and sub-tropical coral reefs
• Ecological dynamics of coral reef ecosystems over broad spatial and temporal scales
• Uncovering shifting baselines to guide reef management actions
• Historical ecology of fishing in Australia
• The origins and evolutionary turnover of Indo-Pacific reef biodiversity

Professor Sean Connolly
Email: sean.connolly@jcu.edu.au

• Species interactions and biodiversity maintenance on coral reefs
• Macroecology, biogeography, and macroevolution of coral reef community structure
• Population dynamics and population viability
• Effects of fishing and marine reserve networks on coral reef fishes
• Metacommunity dynamics and species abundance distributions
• Biodiversity and ecosystem functioning: statistical and theoretical modelling approaches
• Modelling ecological responses to environmental change

Dr. Eugenia Nijgh de Sampayo Garrido
e.sampayo@uq.edu.au

• Coral evolutionary ecology
• Coral symbioses
• Biogeography
• Coral-Symbiodinium specificity
• High latitude and marginal reef symbioses
• Coral reproduction and recruitment

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Coral Reef Oceanography

Professor Ryan Lowe
Email: Ryan.Lowe@uwa.edu.au

My research focuses on how ocean dynamics shape coral reef systems, using a combination of field studies and numerical modelling. Students with quantitative backgrounds in oceanography, the geosciences, or related fields are especially encouraged to discuss research opportunities.

• Hydrodynamics of coral reef systems
• Process-based modelling studies of reef dynamics
• Biophysical interactions within coral reefs
• Coral reef carbonate budgets and response to environmental change
• Mechanisms of coral reef connectivity
• Tropical cyclone impacts on reefs
• Downscaling ocean climate change to local reefs

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Ecological Modelling

Dr Michael Bode
Email: bodem@unimelb.edu.au

• Modelling and understanding complex and uncertain ecosystem dynamics
• The development and maintenance of species coexistence
• Species richness estimators and species distribution models

Professor Sean Connolly
Email: sean.connolly@jcu.edu.au

• Species interactions and biodiversity maintenance on coral reefs
• Macroecology, biogeography, and macroevolution of coral reef community structure
• Population dynamics and population viability
• Effects of fishing and marine reserve networks on coral reef fishes
• Metacommunity dynamics and species abundance distributions
• Biodiversity and ecosystem functioning: statistical and theoretical modelling approaches
• Modelling ecological responses to environmental change

Professor Peter Mumby
Email: p.j.mumby@uq.edu.au

• Future dynamics of coral reefs under climate change and role of management interventions
• Ecosystem function and ecosystem services
• Coral reef resilience. Enquiries to Professor Mumby regarding a PhD scholarship are welcome

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Environmental Governance

Associate Professor Tiffany Morrison
Email: tiffany.morrison@jcu.edu.au

• Quantitative and qualitative analysis of the political dynamics of large scale governance systems
• Longitudinal transformation of large-scale governance systems in tropical, coastal and marine regions
• The role of large organisations (public, private, non-profit) in transformative governance
• Adaptation of governance to large-scale crisis

Dr. Andrew Song
Email: andrew.song@jcu.edu.au

• Human and political geography of fisheries
• Interactive governance and governability
• Multiscalar and transboundary nature of governing tropical, small-scale fisheries
• Stakeholder values, images and principles

Dr. Michele Barnes
Email: Michele.barnes@jcu.edu.au

• Investigating how social networks and social capital drive governance outcomes in marine systems
• Using social-ecological networks to capture linkages and feedbacks in marine governance systems
• Capturing socio-cultural ecosystem service values to improve marine and coastal governance

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Human Dimensions and Social-Ecological Systems

Professor Joshua Cinner
Email: Joshua.Cinner@jcu.edu.au

• Quantitatively examining the socioeconomic drivers of resource use
• Comparative institutional analysis of governance systems used in small-scale fisheries
• Food security in tropical coastal communities
• Assessing social and ecological vulnerability of coastal societies to environmental and policy changes

Dr. Michele Barnes
Email: Michele.barnes@jcu.edu.au

• Investigating how social networks and social capital drive outcomes in marine systems
• Using social-ecological networks to capture linkages and feedbacks in marine social-ecological systems
• Capturing socio-cultural ecosystem service values to improve marine and coastal governance

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 Coral Biology and Ecology

Professor Andrew Baird
Email: andrew.baird@jcu.edu.au

• Coral life histories
• Coral systematics

Dr Mia Hoogenboom
Email: mia.hoogenboom1@jcu.edu.au

• Impacts of climate change on corals and reefs
• Ecological modelling: from individuals to ecosystems
• Effects of pollution on reef organisms
• Trait-based approaches to understanding coral communities
• Ecosystem function of corals

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 Ocean Acidification and Climate Change

Professor Malcolm McCulloch
Email: malcolm.mcCulloch@uwa.edu.au

My research program focusses on the response of corals to climate change and ocean acidification. Students with a background in geochemistry and biochemistry are especially encouraged to discuss research opportunities.

• Quantifying biogenic controls on coral calcification in an acidifying ocean
• Growth and survival of coral at their extreme limits
• Long-term coral proxy records of climate change including ocean acidification, ocean warming and river runoff.
• Role of local versus regional drivers on coral reef ecosystems

Chris Cornwall
Email: christopher.cornwall@uwa.edu.au

• Quantifying the role of environmental variability on marine photosynthetic organisms
• Calcification mechanisms of coralline algae
• Impacts of ocean acidification on seaweed
• Carbon physiology of seaweed

Steeve Comeau
Email: steeve.comeau@uwa.edu.au

• Response of corals and coralline algae to climate change and ocean acidification
• Effects of environmental parameters on calcification mechanisms
• Role of pH variability, light and nutrients
• Up-scaling of calcification from micro-scale (calcification mechanisms) to macro-scale (reef calcification)

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Reef Fish Ecology and Climate Change

Dr Michael Bode
Email: bodem@unimelb.edu.au

• The demographic and evolutionary implications of larval dispersal
• Reconciling different estimation techniques for reef fish dispersal

Dr Hugo Harrison
Email: hugo.harrison@jcu.edu.au

• Dispersal ecology, recruitment dynamics and reproductive success of coral reef fishes
• Connectivity of reef fish populations in the Coral Sea and Great Barrier Reef Marine Park
• Molecular tools for measuring connectivity and dispersal in marine populations

Professor Geoff Jones
Email: geoffrey.jones@jcu.edu.au

• Connectivity of reef fish populations
• Influence of habitat loss on threatened reef fishes
• Behavioural ecology of coral reef fishes
• Role of marine reserves in biodiversity conservation and fisheries
• Coral reef conservation in the coral triangle

Professor Mark McCormick
Email: mark.mccormick@jcu.edu.au

• Climate Change and the Demography of Reef Fish Assemblages

Dr Jodie Rummer
Email: jodie.rummer@jcu.edu.au

My research aims to understand the evolution and functional importance of physiological performance during stress and the impact that changes in water quality and habitat degradation have on marine fishes. Students with a strong background in comparative or ecological physiology and/or biochemistry are preferred. Specific research areas include:

• effects of poor water quality and suspended sediments on coral reef fish development and performance
• the mechanistic basis for enhanced physiological performance under elevated CO2 in coral reef fishes
• the role of habitat in shaping CO2 and temperature tolerance in coral reef fishes
• climate change on early development of tropical elasmobranchs
• tradeoffs between behaviour and physiological performance in reef fishes

Professor Garry Russ
Email: garry.russ@jcu.edu.au

• Fisheries on coral reefs

Dr Jennifer Donelson
Email: jennifer.donelson@jcu.edu.au

My research focuses on how marine fish may respond to future climate change through plasticity. Specific research areas include:

• Developmental and transgenerational plasticity to climate change.
• Behavioural thermoregulation of coral reef fishes
• Acclimation and adaptation of marine fishes to climate change.