In CASE you’re interested: Analysing reefs in 3D

By Dan Bayley

When I joined the London DTP, one of the big draws was that I could create my own PhD topic, and that the partnership worked with organisations like the Zoological Society of London (ZSL), who are highly renowned for their work in my area of interest – marine conservation.

What I didn’t realise at first, was that ZSL is made up of three parts (who knew?): the academically-focussed Institute of Zoology (IoZ); the more project-focussed Conservation Programmes (CP); and then the zoos themselves. With only one of these parts (the Institute of Zoology), being a core partner of the DTP, to work directly with ZSL’s marine conservation team, I would need to think of another plan.

During our PhD training we’d been told about CASE partnerships, and I’d heard of a few people doing them, but it was only really at this point that I thought about trying to organise one. On closer inspection, the bonuses included £1000 each year in addition to your stipend, a period of time spent working with the partner organisation, and co-supervision from your chosen organisation, who are typically looking for more applied results as opposed to purely academic research. It seemed like a no-brainer.

My research looks at threats to shallow tropical coral reefs, as well as ways to quantify and predict future changes, with the aim to inform management for their protection. While some of this work is desk-based, my CASE partner has allowed me to test ideas in the field, using their sites and contacts across the world.

Sharks circle in the Chagos archipelago
Image copyright of Daniel Bayley, used with permission.

My initial period of fieldwork took me to the Chagos archipelago, set right in the middle of the Indian Ocean, roughly 1000 km south of the Maldives. This area is unpopulated across 99% of its 640,000 Km2 of islands, atolls and submerged banks, and is one of the largest marine protected areas in the world, containing some of the most ‘pristine’ marine ecosystems on Earth. Essentially it is top of the ‘bucket list’ for any marine biologist.

We were there to look at the effects of the current El Niño episode, which is heavily impacting marine areas across the world in the third global coral bleaching event on human record.

El Niño Southern Oscillations (ENSOs) are periodic natural events where warm water conditions develop in the Pacific, affecting atmospheric and oceanographic conditions globally. These episodes of sustained altered temperature conditions severely affect ecosystems on land and in the oceans, and their frequency and severity have been gradually increasing as they interact with a globally warming climate. Corals live right at the limit of their thermal tolerance, and changes of just 1-2°C from their ambient condition, if sustained for a number of weeks, will cause the colony to bleach. When a bleaching episode of this magnitude happened in 1998, approximately a fifth of the world’s reefs were lost1.

World Coral Bleaching
Image by NOAA / NESDIS Center for Satellite Applications and Research. Used under a creative commons license.

‘Bleaching’ is a process in which corals expel the symbiotic algae living within their tissues, leaving only a transparent layer covering the white skeleton beneath. The algae, known as zooxanthellae, supply sugars and amino acids to the coral from photosynthesis, and in return are provided shelter and nutrients.

This stress response by the corals occurs as the symbiotic relationship breaks down, typically due to increased temperatures2. In this scenario the symbiotic algae deteriorates and starts producing toxic levels of oxygen; the coral’s response is to digest and ‘spit out’ the algae to save itself further damage. It’s the classic example of a lodger overstaying their welcome, making a mess and not paying the bills. Things are said in the heat of the moment, and now it is time to part ways.


Corals expel their symbiotic algae when temperatures get too high.
Image copyright of Daniel Bayley, used with permission.

During this stressful period, the corals lose their primary source of energy and are more susceptible to disease and infection. Although corals can recover from bleaching by taking new zooxanthellae back into their tissues, if adverse conditions are sustained for a prolonged period, the corals will start to die.

This sensitivity to high temperatures has led to adaptations in some corals to protect themselves, such as selectively absorbing more thermally-tolerant symbionts3. However, the frequency of bleaching episodes is also a key factor in whether the corals die, or live to fight another day, and is set to increase under climate change, creating an ever more pessimistic outlook4.

Data from well-known areas such as the Great Barrier Reef in Australia shows that reefs are declining fast, seeing bleaching across 93% of its range since February, but reefs in remote regions such as the Chagos archipelago are harder to access to collect data and monitor bleaching.

ZSL, along with a consortium of partner institutes from across the world, wanted to see the before and after effects of El Niño on reefs such as the Chagos archipelago, where human influence is limited and relatively natural systems can be observed. You might consider the archipelago a ‘control’ or reference point for observing pressures on reefs across the Indian Ocean region, and a window into how past reefs might have looked and functioned.

Many marine organisms find a home in coral reefs.

Marine organisms find a home in coral reefs.
Image copyright of Daniel Bayley, used with permission.

My particular area of interest was in how the 3D structure of the reef will change following this kind of natural disturbance. The reef’s structure is critical to many ecological processes5, providing food and shelter to organisms such as fish and crustaceans, as well as essential solid substrate for a host of marine organisms.

If the corals, whose skeletons form the solid structure of the reef, are killed by excessive temperatures, the reef as a whole will gradually degrade, eventually becoming ‘flattened’ through biological and physical erosion. Following these types of die-offs, the area can sometimes become dominated by fast-growing algae, making it even harder for the reef to recover – game over for the reef and all the organisms that rely on it6.

And why does it matter if we lose the reefs? Aside from the intrinsic beauty and provision of habitat for marine species, it is estimated at least 500 million people rely directly on tropical reefs for their food and livelihoods. The Great Barrier Reef alone is thought to generate 69,000 jobs and $5.7 billion per year to the economy, just in directly measurable services. That’ll get you more than just a few shrimps for the barbie!

Diving on the Chagos archipelago.

Diving on the Chagos archipelago.
Image copyright of Daniel Bayley, used with permission.

Up until recently our ability to measure the complexity, growth or volume (biomass) of the reef has been limited, leaving us to make only coarse and subjective estimates of changes to the reef. This has made monitoring highly subjective, both in terms of the techniques used and the observer’s frame of reference. It also means that detailed in-situ morphological measurements have not been viable.

The new method we employed to measure the reef uses ‘structure from motion’ photogrammetry techniques to give you a detailed 3D digital rendering of individual colonies, or even whole sections of reef, for future reference and analysis. It’s a bit like putting the reef in for a check-up with a CT scanner after having had a nasty brawl with the local troublemaker ‘El Nino’.

The plan is then to return back to the same locations again next year, following the El Nino bleaching, and assess how the reef has fared in retaining its structure, range of growth forms, and biodiversity. Initial analysis of the impact is stark, with up to 85% of the corals in the reserve thought to have been affected by bleaching.

A 3D reef reconstruction made using structure from motion
Image copyright of Daniel Bayley, used with permission.

But there are also causes for hope. In waters with exceptional clarity such as is seen here, reefs can be found down to 150 m. Using a remote operated vehicle (ROV) we were able to view these ‘mesophotic’ or ‘twilight zone’ reefs. Our surveys focussed around 30 to 60 m and found these deeper ecosystems, away from the hot shallow waters, to be thriving. We also saw still healthy fish populations across the reserve, shark aggregations around the seamounts, and recovering seabird and turtle populations on the islands.

As you might imagine, the remoteness of this location and the equipment needed for this kind of analysis means it would normally be unattainable with a PhD budget alone. Luckily, my CASE partner and their project funder the Bertarelli Foundation allowed me the use of both the equipment and the research vessel needed to carry out this and future work.

My next stop is the central Philippines, where the ZSL partner ‘Project Seahorse’ has helped establish and monitor more than 30 small-scale locally managed marine protected areas over the last 18 years. I’ll be assessing how this management has affected the composition and structure of the reefs in this highly impacted region, where people rely heavily on the reefs for their daily lives. It will be a very different experience to the last trip, but I can’t wait.


Given that the DTP was in its first year when I joined, it wasn’t all easy sailing to arrange and finalise my CASE partnership, but I would recommend it in an instant if you want to open up possibilities for fieldwork and collaborations. In my case at least, I lucked out – my CASE partner has helped take my PhD in new directions, and we even seem to have a thumbs up from the local ghost crab too (if crabs had thumbs)


1. Goreau, T., Mcclanahan, T., Hayes, R. & Strong, A. Conservation of Coral Reefs after the 1998 Bleaching Event. Conserv. Biol. 14, 5–15 (2000).
2. Fujise, L. et al. Moderate thermal stress causes active and immediate expulsion of photosynthetically damaged zooxanthellae (Symbiodinium) from corals. PLoS One 9, 1–18 (2014).
3. Baker, A. C., Starger, C. J., McClanahan, T. R. & Glynn, P. W. Coral reefs: corals’ adaptive response to climate change. Nature 430, 741 (2004).
4. Ainsworth, T. D. et al. Climate change disables coral bleaching protection on the Great Barrier Reef. Science (80-. ). 352, 338–342 (2016).
5. Graham, N. a J. & Nash, K. L. The importance of structural complexity in coral reef ecosystems. Coral Reefs 32, 315–326 (2013).
6. Alvarez-Filip, L., Dulvy, N. K., Gill, J. A., Cote, I. M. & Watkinson, A. R. Flattening of Caribbean coral reefs: region-wide declines in architectural complexity. Proc. R. Soc. B Biol. Sci. 276, 3019–3025 (2009).

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  1. In CASE you’re interested: Analysing reef...
  2. Reef conservation in the Philippines – It’ll blow you away! - The London NERC DTP | The London NERC DTP

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