New PhD opportunity – Dugongs & drone-based photogrammetry

PhD project opportunity
James Cook University, Australia 

Assessing the body size and body condition of dugongs using drone-based photogrammetry

Assessments of individual animal health and condition can signal early signs of population level effects in wildlife from environmental and anthropogenic factors. Animal health assessments relying on wild animal captures can be challenging, hindering our understanding of the wellbeing of populations. In marine mammals, photogrammetry techniques have been applied broadly for measuring body size and estimating body condition of several taxa including manatees. These methods produce reliable body length and nutritional health estimates and can be used to investigate trends in growth and survival, and to identify regional differences in morphometric patterns.

This project will test and validate photogrammetry methods using small aerial drones for accurate morphometric measurements of dugongs’ body size and condition. The student will also utilize this tool in the field to answer different ecological questions relating to nutritional health in dugongs. The student and his supervisory team will work with multiple partners including academics, NGOs, and Traditional Owners and indigenous and non-indigenous land & sea rangers to collect dugong imagery data to identify regional differences in morphometrics of dugongs in places of high dugong conservation value. In return, partners may be trained to conduct drone-based body condition assessment themselves.

The student will be based in the at James Cook University, Townsville, Queensland, Australia, under the supervision of Dr Christophe Cleguer (JCU) and Associate Professor Fredrik Christiansen (Aarhus University). Travel to Europe (Denmark) may be necessary during the course of the PhD.


The successful applicant will have a First Class Honours (or equivalent) in biological science or a related field and will pick up extra points in the scoring system if they have a first authored paper. Preference will be given to those applicants with previous experience in marine mammals’ biology/bioenergetics and evidence of strong bio-statistical and programming skills. Proven experience in working with Indigenous communities is preferred. Journal publications in these fields are desirable but not essential.  Applicants must apply by 25th April, 2023.

Applicants will need to be familiar with the JCU Higher Degree by Research Requirements.

Funding: A 3.5 year stipend scholarship co-funded by JCU and National Environment Science Program (NESP) is provided ($29,900 pa for 3.5 years, tax exempt).  Funds are available to support equipment purchase and initial field implementation.

Contact: Interested applicants should send their 1) CV, 2) academic transcript and 3) a short (max. 1 page) letter outlining their suitability and interest in the project to Dr Christophe Cleguer (

Inshore reef habitats of Great Barrier Reef islands

From coral trout and snapper to wrasses, butterfly fish and damselfish – the inshore reef habitats of Great Barrier Reef islands are known for their complex and rich fish communities.

This month our scientists are conducting visual surveys of reef fishes and benthic habitats of eight inshore island groups in the Great Barrier Reef, building on a 20-year long-term monitoring program at four of the island groups and four new monitoring sites.

The island reefs surveyed are high-value and high-use for tourism and recreational fishing, with areas monitored in no-take marine reserves and zones open to fishing – making the data highly valuable in understanding how fish communities change over time and how they benefit from marine reserves.

Lead researcher Dr Maya Srinivasan said while some reefs were degraded due to past impacts such as cyclones and coral bleaching, many reefs were in great condition with a variety of live coral and fish species.

The inshore fringing reef monitoring seeks to uncover important insights into fish communities in a range of different habitats, including nursery habitats such as mangroves and seagrasses, island fringing reefs, and deeper areas between reefs.

The program is part of the IMR Reef Fish Monitoring Project, funded by the partnership between the Australian Government’s Reef Trust with the Great Barrier Reef Foundation. This is a joint program managed by the Australian Institute of Marine Science, with support from TropWATER, University of the Sunshine Coast, Great Barrier Reef Marine Park and Queensland Agriculture.


eDNA to improve waterway monitoring of invasive and native fish

TropWATER is working with OzFish and the Townsville City Council to use environmental DNA (eDNA) methods to improve waterway monitoring in the Australian tropics.

The project aims to understand what invasive and native species are in key waterways, to help monitor the health of our aquatic systems and improve management.

Lead researcher Dr Cecilia Villacorta-Rath said eDNA was an innovative and cost-effective technique to identify key species without the need of sighting them.

“eDNA analysis can capture the ‘DNA footprint’ that is left in the water – we don’t need to see the species to detect its presence,” she said.

“By collecting water samples and running an analysis in our lab, we can determine what fish species live in the creeks.”

“Long-term eDNA data will give an insight into the fish communities inhabiting these sampled creeks and how these fish communities change through time.”

Citizen science led programs like OzFish and Creekwatch have monitored the health of local creeks in Townsville using methods such as traps and nets in the past, which are labour-intensive and selective, and not able to capture the whole fish biodiversity present in a waterbody.

Dr Villacorta-Rath said eDNA was a valuable tool for these community programs to gain a more comprehensive understanding of the fish species found in these waterways.

“We have run multiple workshops in Townsville, to train community groups on how to take water samples for eDNA analysis.”

“Anyone can take water samples for analysis and it’s great to see so many members of the public get involved.”

More fieldtrips are planned for the Townsville, Herbert, and Burdekin regions. To participate in the next OzFish eDNA sampling event (being held in the Burdekin), please visit:

This project is funded by the partnership between the Australian Government’s Reef Trust and the Great Barrier Reef Foundation and is being delivered in partnership with OzFish Unlimited, James Cook University (TropWATER) and Townsville City Council.




The benefits of converting flood-prone cane paddocks into melaleuca plantations

The common melaleuca ‘paper-bark’ tree could be a powerhouse in not only storing carbon but filtering farm runoff – and farmers and scientists are teaming up to understand how big of an impact these native trees have.

James Cook University’s (JCU) TropWATER Centre’s Dr Adam Canning is working with Ingham farmer John Cardillo and Greening Australia in a project that’s converted 15 acres of flood-prone cane farm into melaleuca plantations.

The project investigates the amount of carbon stored by these plantations compared to non-restored areas, and their role in capturing nutrients from farm run-off mobilised during high rainfall.

Lead researcher Dr Adam Canning said the research looks at how restoration can fit in with the agricultural landscape, where there are benefits for both farmers and the environment.

“Planting melaleuca plantations on flood-prone farms has dual benefits – they are powerful carbon sinks and can help improve water quality,” he said.

“But if agricultural land is restored, it could be at a production loss to farmers, so we need to think about how restoration can have co-benefits for farmers.

“This project is finding the best way to use these flood-prone paddocks to support the long-term success of the agricultural economy by leveraging emerging ecosystem service markets.”

The research involved buring resin bags in the soil for 12 months to measure the nitrate leaching to aquatic ecosystems, as well as assessing soil carbon and microbiome levels.

Canefarmer John Cardillo, who has been involved in various revegetation projects, said the low-lying paddocks were wasted on cane because they were flood prone.

“Revegetating these paddocks is a good way to use this land,” he said.

“These paddocks are so close to the coast – the planted trees are great for holding sediment and it helps with erosion during floods.

“It might seem like a drop in the ocean, but this all adds up.”

Greening Australia’s Sean Hoobin said, “Land which isn’t good for cane can be converted to carbon farming both from vegetation and blue carbon methods – bringing additional income to landholders.”

“Greening Australia’s work with JCU to measure the water quality benefit of melaleuca wetlands, means that farmers may also be able to receive a Reef Credit payment to increase the overall value of restoration.”

Canning said there’s likely many flood-prone cane paddocks in Queensland that can be converted to melaleuca wetlands, and the results from this project could play big role in future restoration initiatives in the agricultural landscape.

“We have also been scoping the potential for planting over 120 other water-tolerant native tree species in locations across the Great Barrier Reef catchment to support carbon sequestration, nutrient runoff treatment and biodiversity.”

This article appeared in Wet Tropic’s Reef and Rivers magazine:



Seagrass restoration project spans two oceans

James Cook University scientists will lead seagrass restoration research spanning tropical Australia’s two oceans.

Researchers from JCU’s Centre for Tropical Water and Aquatic Ecosystem Research (TropWATER) will investigate restoration techniques for key tropical seagrass species, from Queensland’s Great Barrier Reef across to the north of Western Australia.

Their aim is to develop a blueprint for coastal managers to rapidly restore seagrass meadows in high-priority regions.

TropWATER’s Associate Professor Michael Rasheed said future-proofing highly diverse seagrass meadows is crucial to reversing the global downward trend in tropical seagrasses.

“Seagrasses are critical ecosystems,” he said. “They provide habitat for fish, they power coastal marine productivity, and they sequester carbon to help combat climate change – but they’re under increasing pressure from extreme weather events, coastal development and declining water quality.”

Associate Professor Rasheed said climate models predict that future conditions will see more frequent seagrass loss in tropical Australia, making it essential to have tools at hand for effective intervention and restoration.

“We’re investigating the most effective ways to restore different seagrass species, and developing the tools needed for rapid restoration on local and regional levels,” he said.

Professor Rasheed said the project would focus on tropical seagrasses, as most previous seagrass restoration projects have occurred in temperate regions.

Tropical seagrasses can be very different to temperate seagrasses. They have different growth strategies, and they have the potential for much faster recovery once established.

“Some restoration methods applied in temperate systems may not be applicable or transferable to tropical seagrass meadows, which makes our work all the more valuable.

“We’ll investigate methods such as using seeds and cuttings, and new ways they can be used in the field, much the same as many land plants and nurseries operate.”

“We’re going to develop new techniques for tropical seagrass restoration, a blueprint for seagrass-friendly marine infrastructure, and restoration decision tools that can be applied at local and regional scales.”

The project builds on a long-term collaboration with industry partners Ports North and North Queensland Bulk Ports Corporation (NQBP).

“We are proud to support this ground-breaking research that aims to provide practical solutions to safeguard seagrasses and the Reef,” said Simona Trimarchi, NQBP’s Senior Manager of Sustainability and Environment.

The research is a significant next step in TropWATER’s long-term partnership with industry and will benefit from the decades of data already gathered.

“We take our environmental responsibilities seriously,” said Paul Doyle, Ports North’s General Manager of Corporate Affairs and Sustainability. “Together with JCU’s TropWATER Centre we’ve supported seagrass monitoring and research for almost three decades across the ports of tropical Queensland.”

The project is funded by a more than $450,000 Linkage grant from the Federal Government’s Australian Research Council.

Indigenous rangers and scientists team up to drive coral growth

Indigenous rangers and scientists team up to drive coral growth on the Great Barrier Reef during spawning season and beyond.

A team of scientists, First Nations Rangers, tourism operators and conservationists have collected millions of coral sperm and egg bundles at Moore Reef on Gunggandji Sea Country, 50 kilometres offshore from Cairns.

After a week of incubating in custom-designed pools, the coral babies have been  settled out at nearby Hastings Reef, on Yirrganydji Sea Country, in the hope of repairing patches of degraded reef.

The larval delivery project is part of the newly launched reef conservation collective called ‘The Reef Cooperative’, a partnership between Citizens of the Great Barrier Reef, Dawul Wuru Aboriginal Corporation, James Cook University (JCU), Reef Recruits, Mars Sustainable Solutions, GBR Biology and funded by Cotton On Foundation.

The coral larvae project is led by JCU TropWATER and Reef Recruits, who bring years of experience with raising and settling coral larvae and managing complex marine field operations.

JCU’s Dr Katie Chartrand says climate-related disturbances are increasing and the windows for reefs to recover are getting shorter and shorter.

“By using the Great Barrier Reef’s most reproductive time of year – the annual synchronised spawning – we have the potential to significantly boost reef recovery at targeted reef sites,” she said.

“Key to this project is that it’s being delivered with traditional custodians who hold a wealth of knowledge about their local reefs while the research team provides the scientific tools to train those involved.

“This project has been an opportunity to work hand in hand with two local Traditional Owner groups. Sharing our knowledge on spawning and larval rearing is building local capacity to drive conservation outcomes for First Nations peoples across the Great Barrier Reef in the future.”

The team will release 30 million larvae in the project over the next 3 years and build capacity within the community and The Reef Cooperative.

“The transfer of coral larvae from Gunggandji Sea Country to Yirrganydji Sea Country for settling on Hastings Reef is an important opportunity to engage Traditional Owner groups and tell our story about the Great Barrier Reef. Through The Reef Cooperative, we can focus on the Aboriginal cultural heritage dimensions of the Great Barrier Reef, which have not historically been known or told across Australia and the world,” Gavin Singleton, Dawul Wuru Aboriginal Corporation.

These larvae will increase coral coverage over more than 200 square metres of strategically selected degraded reef. The baby corals will have lots of natural predators, but at least 15,000 of them should survive to maturity.

”It’s a privilege to work on this project in collaboration with Traditional Owners. It’s also exciting to be trialling new methods to increase the coverage of high-density larval delivery,” said Dr Kerry Cameron, Reef Recruits.

This project spans two different sea countries, which is only possible thanks to the support and collaboration of the Gunggandji and Yirrganydji people. Gunggandji Elders say Moore Reef has long been known to them as a source reef and they have a strong spiritual connection with it.

“The fusion of Traditional Owner Ecological Knowledge with modern science for the whole world to see and be part of is what the mutually beneficial partnership of the Reef Cooperative is all about, and provides hope for the World Heritage Great Barrier Reef for generations to come,” said Eric Fisher, GBR Biology.

Tim Diamond, GM of Cotton On Foundation says, “Through our partnership with Citizens of the Great Barrier Reef, we are proud to be the founding funders of The Reef Cooperative and supporting the important cultural and conservation milestones for Hastings Reef on Yirrganydji Sea Country. The Reef Cooperative is a unique conservation model in action, driven by innovation and knowledge sharing between Traditional Owners, scientists and conservationists that can help protect and conserve the Great Barrier Reef. We’re looking forward to mobilising our customers and supporters in reef conservation over the next three years of The Reef Cooperative journey.”

Yirrganydji rangers have supported the fieldwork to prepare the delivery site at Hastings Reef and rangers from both groups will help with the collection of coral spawn and raising of the larvae.

Dugong Census Begins

James Cook University scientists are in the air conducting critical Queensland-wide dugong population survey – counting dugongs along 2000 kilometres of coastline in under two months.

Like a census, the surveys are conducted over an intense period every five years to get a snapshot of dugongs and calves’ populations, from Cape York to Moreton Bay.

JCU TropWATER’s Dr Chris Cleguer said Australia is home to the largest dugong population in the world, and the surveys are critical for monitoring trends in abundance and distribution.

“These aerial surveys have been conducted for more than 30 years and are essential in not only estimating the current dugong population size but also mapping where dugongs are more or less abundant,” he said.

“There are concerns about the decline in dugongs across the urban coast of the Great Barrier Reef – this year’s surveys will give us the opportunity to understand the extent of this.”

Hervey Bay to the south of the Great Barrier Reef, a known hot spot for dugongs, is an area of concern following a major loss of seagrass habitat earlier this year. The seagrass loss resulted from two flood events, which smothered the seagrass and destroyed the dugongs’ main food source.

“The surveys will help us to determine how many dugongs currently are in Hervey Bay and the Great Sandy Strait as well as understanding their large-scale movements,” he said.

“It is possible the dugongs have moved in search of seagrass to other nearby key habitats such as Gladstone to the north or Moreton Bay to the south.”

Dr Cleguer said, for the first time in Queensland, the aerial surveys will also use cameras attached to one of the legs of the aircraft to capture thousands of images of the water surface.

“These large-scale aerial surveys usually rely solely on highly trained observers to count dugongs from the sky,” Dr Cleguer said.

“But our collaborative research group is transitioning to using imagery survey and artificial intelligence to track and monitor dugongs in the future – saving time, money and providing enhanced data.”

The Great Barrier Reef dugong population aerial surveys are one of the critical Reef monitoring projects funded by the partnership between the Australian Government’s Reef Trust and the Great Barrier Reef Foundation (Cape York to Bundaberg). The surveys in Queensland’s southern bays, Hervey Bay and Moreton Bay, are also funded by the Department of Climate Change, Energy, the Environment and Water.

Great Barrier Reef Foundation Managing Director Anna Marsden said incorporating new technologies like AI is key to accelerating impact in tracking the health of the Reef and its animals.

“Dugongs are not only a vulnerable marine species we must protect, they’re also a priority indicator species for climate change and ecosystem health, with dugongs’ in-shore seagrass nurseries and feeding grounds highly susceptible to climate change impacts,” Ms Marsden said.

“By using new technologies and supporting efforts to accelerate and advance the aerial dugong surveys with our research partners from JCU, we will be able to give Reef managers and researchers access to the best possible information to proactively manage and protect the Reef and its marine life.”

The research team will survey from the Cairns region south to Moreton Bay over the next two months, and further surveys are planned for Cooktown to Cape York in 2023.


Bringing back bushfoods: Australia’s landscape mapped to boost bush tucker

Growing native bushfoods could reverse environmental degradation and offer better food security. But how do we get bushfoods in the agricultural sector in a market saturated by modern crops?

New research from James Cook University’s TropWATER has mapped Australia’s entire landscape to uncover the best places to grow more than 170 bushfoods.

The study found the Great Barrier Reef catchment area to be a hotspot for a wide range of bushfoods including those most in-demand commercially, including lemon myrtle, native plums and bush tomatoes.

Author Dr Adam Canning said identifying what native crops can grow where was an important first step in scoping potential native food industries to support farmers.

“Native foods in Australia have a rich history and there is a growing demand to get bushfoods in the supermarket, yet the commercial production of native foods remains small,” he said.

“This research maps Australia’s entire landscape to identify exactly what bushfoods can be grown where – and that’s a big step toward boosting Australia’s native food industry.”

Dr Canning said transitioning the agricultural landscape to include a diversity of native bushfoods would help reverse environmental degradation.

“Modern non-native crops such as sugarcane and wheat need intensive cultivation, irrigation, herbicides, and pesticides, and are grown as monocultures,” he said.

“This comes at a cost to the environment, and we’ve seen this happen along the Great Barrier Reef catchment.

“Diversifying modern agricultural systems to include native plants would help restore balance in coastal ecosystems through reducing runoff, improving soil health and supporting biodiversity.”

Coastal areas of Queensland’s wet tropics, south-east Queensland, New South Wales, and Victoria were predicted to support the greatest diversity of native food and forage species.

“These areas are the most agriculturally intensive areas with degraded environments, but they also have the greatest potential for regenerative agricultural practices,” he said.

“Farmers could start small by trialling intercropping, and slowly expand as knowledge and industries grow.”

To further incentivise these practices, more financial benefit schemes need to be developed to reward farmers for providing ecosystem services, such as carbon sequestration and reduced pollution.

The research also indicates a significant opportunity for Indigenous-led business models within the emerging bush foods sector. However, steps would need to be taken to ensure Indigenous knowledge and intellectual property are protected.

The research paper Rediscovering wild food to diversify production across Australia’s agricultural landscapes was published in Frontiers in Sustainable Food Systems.


Women Warriors of the Torres Strait set sail for the Great Reef Census  

The Women Warriors of the Torres Strait – an all-female crew of Traditional Owners, rangers and scientists led by the Torres Strait Regional Authority (TSRA) Sea Team and James Cook University – has set sail as part of the Great Reef Census to survey the northernmost section in the Torres Strait, northern Australia.

The five-day voyage to Mer (Murray Island) by the Women Warriors of the Torres Strait is the first time the Great Reef Census – led by Citizens of the Great Barrier Reef – has ventured beyond Cape York.

TSRA Senior Natural Resource Management Officer and Marine Biologist Madeina David, 24, said the trip served as ‘ethical science’ in the Torres Strait, with researchers and Traditional Owners working together to monitor the Great Barrier Reef, collect data and share findings with island communities to support local decision making.

“Our voyage sets a new course for science to value, respect and incorporate the traditional ecological knowledge of custodians who have cared for land and sea for centuries,” Ms David said.

“We will connect ancient knowledge and modern science to assess the condition of the northern Great Barrier Reef, including water temperatures, coral conditions and even explore the potential for a future turtle sanctuary.”

TSRA Sea Team Manager Moni Carlisle said checking conditions, including marine habitat at Mer, would provide critical insight into the future of the Great Barrier Reef.

“The Torres Strait is the northern tip of the Great Barrier Reef and known as the seagrass capital of the world. As home to globally important marine migratory species, including dugong and sea turtles, it is proving to be vital to the future of the Great Barrier Reef for both corals and sanctuary for species recovery,” she said.

JCU TropWATER’s Dr Katie Chartrand said the expedition was a valuable opportunity to work in partnership with Traditional Owners and rangers to paint a clearer picture of this hotspot of reef biodiversity.

“Using the Great Reef Census, we can rapidly collect thousands of reconnaissance images of remote reefs that have rarely or never before been formally surveyed,” she said.

Dr Chartrand said concerns have been raised of potential outbreaks of crown-of-thorns starfish, flagging the importance to survey this pristine region of the Great Barrier Reef.

“This Census gives TSRA and the local Meriam community a snapshot of the health of the reef habitats – and that’s a powerful strategy in taking steps to protect these extraordinary reefs.”

The Women Warriors of the Torres Strait Great Reef Census voyage is funded by the TSRA and supported by partners including the Citizens of the Great Barrier Reef and James Cook University.

Spearfishing restrictions boost fish stocks

Restricting spearfishing in some ‘yellow zones’ in the Great Barrier Reef Marine Park has doubled the abundance of coral trout, according to new research led by James Cook University scientists.

The study published in Biological Conservation focused on reefs around the Capricorn Bunkers, offshore from Gladstone, looking at the abundance of targeted fish species in partially protected Marine Park Zones known as ‘yellow zones’.

Researchers compared yellow zones that allow spearfishing to ‘special management area’ yellow zones that prohibit spearfishing.

JCU’s TropWATER scientist Dr April Hall said while spearfishing can be an ecologically sustainable activity with minimal bycatch, restricting the activity via designated spearing-free management zones can have conservation benefits at a regional scale.

“What we found was in yellow zones that excluded spearfishing, the numbers of target species such as coral trout were significantly higher compared to fishing zones that allow spearfishing,” she said.

“These restricted yellow zones also rivalled the abundance in nearby protected no-take green zones.

“Regardless of the effects of spearfishing, both kinds of yellow zones still support a greater abundance of coral trout compared to nearby blue zones, where fishing is less restricted.”

Dr Hall said while this study showed the conservation benefits of prohibiting spearfishing, it’s not necessarily the case across the entire Great Barrier Reef.

“We’ve compared other yellow zones in different parts of the Great Barrier Reef and the outcome varies, most likely due to differences in the popularity of spearfishing.”

JCU’s Professor Mike Kingsford said no-take marine reserves were one of the most effective conservation measures to restore the abundance of fish.

“Fully protected green zones in the area support the most significant number of large coral trout,” he said.

“This is a really important protection measure because large coral trout change sex from female to male, and this helps to maintain healthy breeding populations.”

Co-author, Great Barrier Reef Marine Park Authority’s Director Darren Cameron said the research demonstrated that yellow zones were an important marine park management tool providing a balance between conservation and sustainable fishing activities.

“Healthy fish populations in both yellow zones and protected no-take green zones produce baby fish, many of which grow up and are subsequently caught throughout fished areas. These zones improve fishing, with more fish also importantly contributing to the health and resilience of the entire Great Barrier Reef,” he said.

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