People and ecosystems

Understanding of the links between coral reef ecosystems, the goods and services they provide to people, and the wellbeing of human societies.


Ecosystem dynamics: past, present and future

Examining the multi-scale dynamics of reefs, from population dynamics to macroevolution


Responding to a changing world

Advancing the fundamental understanding of the key processes underpinning reef resilience.

Coral Bleaching

Coral Bleaching

Coral Reef Studies

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

Phone: 61 7 4781 4000
Email: info@coralcoe.org.au

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A new study on the effects of climate change in five tropical countries has found fisheries are in more trouble than agriculture, and poor people are in the most danger.

Distinguished Professor Joshua Cinner from James Cook University’s ARC Centre of Excellence for Coral Reef Studies led the study. He said tropical regions are expected to suffer losses in both fisheries and agriculture as the effects of climate change increasingly make themselves felt.

“For example, by 2100 tropical areas could lose up to 200 suitable plant growing days per year due to climate change. Likewise, in some tropical areas fishable biomass in the ocean could drop by up to 40 per cent,” said Professor Cinner.

“Yet assessments of climate change impacts and the policy prescriptions that come from them rarely consider changes to agriculture and fisheries simultaneously, and those that do are at the national scale.

“These larger-scale assessments gloss over how households and even entire communities will be affected by climate change.”

Prof Cinner led a team of 28 researchers who investigated the potential impacts of climate change on agriculture and fisheries for 72 coastal communities across Indonesia, Madagascar, Papua New Guinea, the Philippines, and Tanzania.

The authors integrated socioeconomic surveys from over 3,000 households with model projections of losses to crop yield and fisheries catch under a high emissions scenario (SSP 5–8.5) and a low emissions scenario (SSP 1–2.6).

They found that, although different communities vary in how vulnerable they are both within and across countries, the communities with lower socioeconomic status are particularly exposed to severe impacts and have higher dependence on natural resources, so these impacts will hit harder.

“We found that the potential losses are expected to be higher in the fisheries sector than agriculture overall, but the big problem is that two thirds of the communities we studied will experience potential losses to both fisheries and agriculture simultaneously, under a high emissions scenario,” said Professor Cinner.

“Our in-depth surveys revealed that many people have limited opportunity to adapt to changes by switching livelihoods between food production sectors.

“But climate change mitigation – reducing greenhouse gas emissions – could reduce the proportion of places facing that double burden by half.

It really does show how much the lives of very many ordinary people hinge on decisions they have no control over and highlights the moral responsibilities that decision makers have towards them,” said Professor Cinner.


Cinner JE, Caldwell IR, Thiault L, et al. 2022. ‘Potential impacts of climate change on agriculture and fisheries production in 72 tropical coastal communities’. Nature Communications. DOI: 10.1038/s41467-022-30991-4


Professor Joshua E. Cinner (Townsville, AEST)
P: +61 (0) 747 816 751
E: joshua.cinner@jcu.edu.au

James Cook University researchers have found brightly coloured fish are becoming increasingly rare as coral declines, with the phenomenon likely to get worse in the future.

Christopher Hemingson, a recent PhD graduate at JCU’s Centre of Excellence for Coral Reef Studies, led the research. He said over the past 30 years, human-induced stressors have caused profound changes to reefs – typically from the loss of corals.

“Reefs these days are becoming increasingly defined by non-coral substrates, especially turf algae. We wanted to investigate what effect this had on the kind of brightly-coloured fish people like and that attract tourists and visitors,” said Dr Hemingson.

The scientists used a new community-level measure of fish colouration and then explored the links between fish community colouration and the environment.

“We found that as the cover of structurally complex corals increases on a reef, so does the diversity and range of colours present on fishes living in and around them. But, as the cover of turf algae and dead coral rubble increases, the diversity of colours declines to a more generalised, uniform appearance,” said Dr Hemingson.

He said it was notable that fish community colouration declined significantly in the years following the 1998 global coral bleaching event – likely driven by the loss of branching corals.

“We found the structure of the sea floor appears to be very important in shaping fish colouration; more so than its composition (that is, its live coral cover). Having places to hide from predators may have allowed reef fishes to evolve unique colourations due to a reduced reliance on camouflage to avoid being eaten.

“Unfortunately, the types of corals most capable of surviving the immediate impacts of climate change (massive and boulder corals) are unlikely to provide these refuges. Fish communities on future reefs may very well be a duller version of their previous configurations, even if coral cover remains high,” said Dr Hemingson.

He said the loss of colourful fishes may not have a huge impact if assessing reefs through a strictly functional or ecological lens.

“But in a human context, loss of these colourful species may trigger a broad range of human responses, including grief.”



Hemingson CR, Mihalitsis M, Bellwood DR 2022. ‘Are fish communities on coral reefs becoming less colourful?’. Global Change Biology. DOI: 10.1111/gcb.16095


A selection of images can be used for media stories with credit to the photographer as stated in the file name. Please note these are for single use with this story only, not for any other story. No archival permissions are granted.


Dr. Christopher Hemingson (Townsville, AEST)
P: +61 (0) 450 848 901
E: christopher.hemingson@my.jcu.edu.au

Researchers have discovered some good news for fish populations living on coral reefs hit by climate change.

Renato Morais is a PhD candidate from the ARC Centre of Excellence for Coral Reef Studies (Coral CoE) at James Cook University (JCU). He led a study that looked at how fish on a bleached coral reef get their food.

“We already knew that coral reef fish rely on food drifting in from the sea, such as plankton,” Mr Morais said.

“But, we didn’t know exactly how important this was,” he said.

Mr Morais and Professor David Bellwood, also from Coral CoE at JCU, combined high-resolution surveys and individual biomass production estimates to generate the first map of where the energy comes from for all fish on a coral reef.

“We looked at everything from gobies to coral trout and large jacks, assessing more than 18,000 fish from over 300 species,” said Mr Morais.

“We found that various transport mechanisms, such as currents and tides, interact with the reef and bring in vast amounts of plankton.”

The pair found that for every kilogram of fish produced on the reef more than 400 grams of that kilogram relied on food derived from the open ocean, rather than the reef itself. This rises to almost 600 grams on the side of the reef facing the open ocean.

“This means, that for many reefs, food from outside can sustain fish populations, even when the coral is badly damaged,” Prof Bellwood said.

The scientists found that areas of the reef that were more exposed to the open ocean produced the largest quantities of fish – with reef slopes being the most fruitful.

“The discovery that reef fish get so much of their food from off-reef sources was encouraging, especially because many species that feed on oceanic material have a history of disappearing after coral loss,” said Mr Morais.

“This is the first time we have been able to put all species in perspective,” said Prof Bellwood. “Our study offers hope that reefs subject to coral loss can still be productive.”

“The reefs may be damaged but they are still incredibly valuable.”

The study is published today: Morais R and Bellwood D (2019). ‘Pelagic Subsidies Underpin Fish Productivity on a Degraded Coral Reef’. Current Biologyhttps://doi.org/10.1016/j.cub.2019.03.044



Renato Morais
E: Renato.morais@my.jcu.edu.au
M: 0467 479 297



An international team of researchers has mapped Nemo’s genome, providing the research community with an invaluable resource to decode the response of fish to environmental changes, including climate change.

In a breakthrough study led by the King Abdullah University of Science and Technology (KAUST) and the ARC Centre of Excellence for Coral Reef Studies (Coral CoE), researchers used high-tech sequencing tools to create one of the most complete genetic maps for the orange clownfish, a common reef inhabitant and star of the Disney movie, Finding Nemo.

“This genome provides an essential blueprint for understanding every aspect of the reef fish’s biology,” said lead author Dr Robert Lehmann of KAUST in Saudi Arabia.

“It contains 26,597 protein coding genes. And like the world’s largest jigsaw puzzle, it took patience and time to assemble.”

The orange clownfish, Amphiprion percula, is not only the most recognized reef fish on Earth, but also one of the most highly studied.

“This species has been central to ground-breaking research in the ecological, environmental and evolutionary aspects of reef fishes,” said co-author Professor Philip Munday of Coral CoE at James Cook University in Australia.

“For example, the clownfish is a model for studying sex change in fishes. It has also helped us understand patterns of larval dispersal in reef fishes and it’s the first fish species for which it was demonstrated that predator avoidance behaviour could be impaired by ocean acidification.”

The team used state-of-the-art technology to sequence the clownfish’s genome. Their genomic and transcriptomic data is now available via the Nemo Genome DB database.

“The clownfish comprises approximately 939 million nucleotides that needed to be fit together,” said co-author Professor Timothy Ravasi of KAUST.

“This is an extremely valuable resource for the research community and will further establish the orange clownfish as an ideal lab subject for genetics and genomic studies.”

“This is one of the most complete fish genomes ever produced,” said co-author Professor David Miller of Coral CoE at James Cook University.

“Using the PacBio single molecule, real-time sequencing technology, enabled us to achieve a polished result.”

The paper “Finding Nemo’s Genes: A chromosome-scale reference assembly of the genome of the organge clownfish, Amhiprion percula” is published today in the journal Molecular Ecology Resources.

Images available here.


This research is dedicated to the memory of Dr Sylvain Forêt, a brilliant scientist, co-author, colleague and friend. (Tribute, pg. 10)


Citation: Lehmann, R, Lightfoot, D.J., Schunter, C., Mitchell, C.T., Ohyanagi, Mineta, K., Foret, S., Berumen, M.L., Miller, D.J., Aranda, M., Gojobori, T., Munday, P.L., and Ravasi, T. (2018) Finding Nemo’s Genes: A chromosome-scale reference assembly of the genome of the orange clownfish Amphiprion percula. Molecular Ecology Resources




Prof Philip Munday

Coral CoE

P: +61 (0) 0408 714 794, +61 (0)7 4781 5341 (AEST/ GMT +10)

E: philip.munday@jcu.edu.au



Dr Robert Lehmann


E: robert.lehman@kaust.edu.sa


Prof Timothy Ravasi


P: +61 (0) 491333697 (PDT/ GMT -7)

E: timothy.ravasi@kaust.edu.sa



Catherine Naum

Communications Manager

ARC Centre of Excellence for Coral Reef Studies

P: +61 (0) 0428 785 895, +61 (0)7 4781 6067 (AEST/ GMT +10)

E: Catherine.Naum1@jcu.edu.au


Michelle Ponto

Communications – Editorial and Global Media Manager

King Abdullah University of Science and Technology

P: +966 (54) 470 1668 (AST/ GMT +3)

E: michelle.ponto@kaust.edu.sa




Many coral reefs will be unable to keep growing fast enough to keep up with rising sea levels, leaving tropical coastlines and low-lying islands exposed to increased erosion and flooding risk, new research suggests.

An international team, led by scientists from University of Exeter, Royal Netherlands Institute for Sea Research, Lancaster University and the Australian Research Council’s Centre of Excellence for Coral Reef Studies (Coral CoE), compared the maximum upward growth rates of coral reefs with predicted rates of sea-level rise, and found many reefs will be unable to keep pace.

The growth of coral reefs is strongly influenced by the amount and types of coral living on the reef surface. This growth is now being hampered by combinations of coral disease, deteriorating water quality and fishing pressure, along with severe impacts from “coral bleaching” caused by climate change.

“For many reefs across the Caribbean and Indian Ocean regions, where the study focused, rates of growth are slowing due to coral reef degradation,” said lead author Professor Chris Perry, of the University of Exeter.

“Meanwhile, rates of sea-level rise are increasing – and our results suggest reefs will be unable to keep up. As a result, water depths above most reefs will increase rapidly through this century.”

“Even under modest climate change prediction scenarios (RCP4.5) only about 3% of Indian Ocean reefs will be able to track local sea-level rise projections without sustained ecological recovery, whilst under continued high emission scenarios (RCP8.5) most reefs will experience water depth increases in excess of half a metre,” added co-author Dr Aimée Slangen of NIOZ, Royal Netherlands Institute for Sea Research.

“This is now of critical concern because reefs play a key role as natural sea defences by limiting coastal wave energy exposure,” commented Professor Nick Graham, of Lancaster University, another co-author of the study.

“Efforts to tackle climate change must therefore be coupled with careful management of fishing and water quality protection to prevent widespread submergence through this century.”

The researchers calculated growth rates for more than 200 tropical western Atlantic and Indian Ocean reefs.

“Now more than ever, we must limit global greenhouse gas emissions. Our predictions, even under the best case scenarios, suggest that by 2100 the inundation of reefs will expose coastal communities to significant threats of shoreline change,” said co-author Professor Peter Mumby of Coral CoE at The University of Queensland. “Healthier coral reefs will reduce the rate of seawater inundation.”

Professor Perry concluded: “The most worrying end-point scenario in this respect is that if predictions of increasing bleaching frequency are realised, many reefs may become locked into permanent low growth rate states, leading to more submergence under all future sea-level rise scenarios.”

The paper, published in the journal Nature, is entitled: “Loss of coral reef growth capacity to track sea-level rise under climate change.”

Citation: Perry, CT, Lorenzo, A-F, Graham, NAJ, Mumby, PJ, Macdonald, C et al. (2018). Loss of coral reef growth capacity to track future increases in sea level. Nature1476-4687 DOI – 10.1038/s41586-018-0194-z

Videos and images available here. Please credit all files to: Prof Chris Perry, University of Exeter, as indicated in the captions document.

Contacts for interviews:

Professor Nicholas Graham
Lancaster University, Lancaster Environment Centre
P: +44 (0) 7479 438 914 (GMT/UTC)
E: nick.graham@lancaster.ac.uk

Professor Peter Mumby
The University of Queensland
P: +61 7 3365 1686 or 0449811588 (AEST/UTC +10)
Email: p.j.mumby@uq.edu.au

For more information:

University of Exeter
Press Office
+44 (0)1392 724828

Catherine Naum
Communications Manager, ARC Centre of Excellence for Coral Reef Studies
P: +61 (0)7 4781 6067 or +61 (0) 428 785 895 (AEST/UTC +10)
E: catherine.naum1@jcu.edu.au


Scientists typically make every effort to keep all factors but one constant when doing an experiment. Global-change scientists might move a coral from a reef to an aquarium whose water is held 1°C higher to test the effects of the ocean warming predicted for the end of the century. Or they might decrease the water’s pH by 0.4 units to study the effects of ocean acidification.

But a new review article presents evidence that argues for a more nuanced approach to the design of these experiments–one that acknowledges and purposefully incorporates the variability inherent in nature.

The article, in the latest issue of Current Climate Change Reports, focuses on studies examining how ocean warming and acidification might affect corals and coralline algae. Lead author Emily Rivest of William & Mary’s Virginia Institute of Marine Science (VIMS) says its findings are also likely applicable to other foundational reef species such as oysters.

“The range of pH and temperature that some organisms experience on a daily basis exceeds the changes we expect to see in the global ocean by the end of the century,” notes Rivest, an assistant professor at VIMS. “But we don’t really know how this variability affects their physiology and their ability to respond to future change. The papers we reviewed suggest this variability is important, and we need to incorporate it into our experiments.”

Indeed, there’s a growing consensus that the degree of variability in temperature and pH an organism faces in its current environment will likely influence its response to future warming and acidification. For instance, a coral growing in a back-reef lagoon–whose restricted waters may warm drastically each afternoon under the blazing sun–may be less susceptible to long-term warming than a coral growing in the more open, temperate waters of the reef face. The same may hold true for entire species or populations of warmth-adapted corals.

In their paper, Rivest and co-authors Drs Steeve Comeau and Christopher Cornwall from the ARC Centre of Excellence for Coral Reef Studies (Coral CoE) and The University of Western Australia reviewed almost 100 studies of how predicted changes in ocean pH or temperature might affect coral growth. But their review found only a “handful” of the studies had purposefully varied these factors, or examined the importance of natural variability to the performance of reef organisms.

The experiments that incorporated variability fell into two categories. “One type was studies where you collect corals from a high-variability site and a low-variability site and see how they do under controlled laboratory conditions,” says Rivest. “If the variability is important in shaping their response to environmental change, then their response will depend on the site they are from.”

The second type “looked at the variability within laboratory treatments–taking corals into the lab and raising them under constant or variable conditions, then providing them with an additional stress and seeing if the variability they experienced in the lab influences their response to that stress.”

Rivest and her colleagues found that incorporating variability into an experiment’s design produced ambiguous and intriguing results.

“Corals from habitats with more temperature variability generally exhibit greater thermotolerance,” says Rivest, “but the effects of past pH variability are less clear.” On the other hand, she says, “In laboratory studies, pH variability often limited the effects of ocean acidification, but the effects of temperature variability on responses to warming were equivocal.”

Rivest, Comeau, and Cornwall say their findings warrant additional research. “We want our paper to signal the start of a new era in studies of how climate change affects foundation species,” says Rivest. “We really need to consider an animal’s current environment as a starting point for how it will respond in the future–we want this to be a point of discussion in our field, for how we should be designing experiments and thinking about these questions moving forward.”

The team says their findings could also lead to practical applications. “If we know better how environmental variability affects the ability of animals to tolerate future environmental change, then we can think about it in a restoration and conservation context,” says Rivest. “For example, if you target a reef for restoration, we could start a training program for corals where you culture them in the lab under variable conditions so they would be ready to perform well out in the reef environment.” This approach is already being applied at the Hawai’i Institute of Marine Biology, the Australian Institute of Marine Science, and other research labs worldwide.

The paper “The Role of Natural Variability in Shaping the Response of Coral Reef Organisms to Climate Change” is now available online.



Mr David Malmquist
Communications Director
Virginia Institute of Marine Science, VA USA
E: davem@vims.edu
P: +1 804-684-7011

Dr Chris Cornwall
Research Fellow
University of Western Australia, Perth Australia
E: christopher.cornwall@uwa.edu.au
P: +61 (0) 8 6488 3644

Marine scientists at The University of Queensland’s Global Change Institute and the ARC Centre for Excellence in Coral Reef Studies have shown that local human activities negatively influence coral reef ecosystems in a series of complex interactions, some of which are poorly understood by science.

A detailed underwater study was undertaken at 26 sites across the Maldives, south-west of India, as part of a XL Catlin Seaview Survey.

The scientists investigated coral reef communities adjacent to human populations ranging from zero to more than 150,000 people.

PhD candidate Kristen Brown said although marine scientists already knew human activity placed pressure on coastal reef systems, the extent to which these impacts were translated to impacts on coral reefs via changes to coral-algal competition had rarely been investigated.

“We’ve demonstrated that local human populations have a strong influence on coral reefs,” Ms Brown said.

“Many people believe that isolated reefs, near relatively small human populations, are healthier.

“Our study, however, noted a decline in certain categories of reef-building corals and an increase in dead coral and filamentous algae on reefs adjacent the densest human communities.

“Importantly, this study only provides a snapshot into the interactive dynamics of coral and algae, and seasonal and long-term investigations should be implemented.

“The results of our study have implications for the effects of human populations on coral reef communities, drawing attention to how these drivers influence reef processes such as coral-algal competition,” Ms Brown said.

Associate Professor Sophie Dove from the ARC Centre for Excellence in Coral Reef Studies at The University of Queensland said understanding these changes was becoming more and more important as global changes due to ocean warming and acidification increase.

“Understanding how these changes interact is going to be increasingly important especially as we see more frequent impacts like that of the mass coral bleaching across the Maldives in 2016,” Dr Dove said.

“This may help coral reef managers target their interventions with better outcomes.”

XL Catlin Seaview Survey Chief Scientist Professor Ove Hoegh-Guldberg said the project had enabled some of the largest ecological measurements of reef health.

“Projects such as this will allow us to put down important baselines against which we can measure progress against goals,” he said.

The XL Catlin Seaview Survey began on the Great Barrier Reef in September 2012. Following successful Great Barrier Reef and Coral Sea surveys, the project was rolled out globally thanks to the ongoing support of founding sponsor, global insurance group – XL Catlin Group Limited.

In 2014 the major campaign area was the waters of South-East Asia, while in 2015 the reefs of the Indian Ocean, including the Maldives, were surveyed. The team has recorded additional survey areas, including the Galapagos Islands, and temperate water locations including Monaco and Sydney.

Download the research paper cited above.


Kristen Brown, kristen.brown@uq.edu.au

Global Change Institute Communications, gcicomms@uq.edu.au +61 (0) 438 285 283

New research examining the possible impacts of ocean acidification provides fresh hope for the survival of reef fish.

Just as when a camera lens comes into focus, the latest research published today sharpens understanding of the implications of ocean acidification on reef fish behaviour, yielding promising results for their current and near-future survival.

Chemical changes in the ocean, as a result of climate change, are leading to a more acidic environment, referred to as ‘ocean acidification’ (OA). In a laboratory setting, these changes have been shown to lead to a range of risky behaviours in the affected fish, with some fish unable to flee from their finned foes effectively.

But, when researchers recalibrated experiments to adjust for natural daily changes in concentrations of dissolved carbon dioxide (CO2), the primary chemical driver of OA, they found that the fish were less affected than previously thought.

“Shallow water habitats where reef fish live can experience substantial natural fluctuations in water chemistry throughout the day,” explained senior author Professor Philip Munday, of the ARC Centre of Excellence for Coral Reef Studies (CoralCoE) at James Cook University.

“For example, carbon dioxide levels on coral reefs are often much lower during the day than they are at night.

“Our data suggests that these natural daily changes in water chemistry are enough to provide fish with a recovery period, reducing their sensitivity to higher carbon dioxide levels,” said Michael D. Jarrold, lead author of the study and PhD student at James Cook University.

The study published today in Scientific Reports, utilised state-of-the-art facilities at James Cook University and at the Australian Institute of Marine Science’s National Sea Simulator (SeaSim) to mimic the natural conditions of a coral reef environment.

“It’s the first time these dynamic natural conditions have been reproduced in a laboratory setting to test  their potential influence on the behaviour of coral reef fish,” explained Mr. Jarrold.

“We are thrilled about what we’ve found,” he added. “Our results provide a greater level of optimism for reef fish populations in the future.”

Previous OA research has largely used stable, open ocean conditions to guide the experimental design.

“Broadly speaking, such studies reported reduced anti-predator responses, as compared with the control group,” said Prof Munday.

“Such abnormal behaviours were feared to pose significant ecological consequences for fish populations,” he explained.

The researchers’ ability to precisely control the complex combinations of environmental variables required to accurately simulate both naturally occurring and human-influenced water conditions was crucial to achieving this breakthrough.

“With the world’s most advanced experimental marine technology at our finger tips, and the considerable efforts of our specially skilled team, the SeaSim was able to recreate the natural daily CO2 cycles found on the reef,” said Craig Humphrey, co-author and SeaSim precinct manager at the Australian Institute of Marine Science.

“We’re excited to play a part in such fantastic and novel research.”

The paper titled: “Diel CO2 cycles reduce severity of behavioural abnormalities in coral reef fish under ocean acidification” is available online at:




Images must carry credits as listed in Dropbox folder




Prof Philip Munday
ARC Centre of Excellence for Coral Reef Studies
Phone: +61 (0) 0408 714 794, +61 (0)7 4781 5341 (AEST)
Email: philip.munday@jcu.edu.au

Mr Michael D. Jarrold
James Cook University
Email: michael.jarrold@my.jcu.edu.au



Ms Catherine Naum
Communications Manager
ARC Centre of Excellence for Coral Reef Studies
Phone: +61 (0) 0428 785 895, +61 (0)7 4781 6067 (AEST)
Email: Catherine.Naum1@jcu.edu.au


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ARC Centre of Excellence for Coral Reef Studies
James Cook University Townsville
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Phone: 61 7 4781 4000
Email: info@coralcoe.org.au