Saving corals from silent extinctions requires a new approach

In the clear, tropical waters surrounding the Palm islands in the central Great Barrier Reef lagoon, Dr Tom Bridge dives down to a coral colony with antler-like, bottle brush branches  – a common shape in the Acropora family. As he carefully chisels away a hand-sized sample, he wonders if the DNA from its live tissue will prove it to be the same species described from a sample collected here 130 years ago – the bleached, lifeless skeleton stored in the Natural History Museum, London – or perhaps it will be a new species?

Bridge’s unique research is redefining our understanding of reef coral diversity, with important implications for conservation; for how can we conserve corals if we don’t accurately know which species grow where? 

Acropora, or Staghorn corals, are abundant on tropical and subtropical reefs across the Indo-Pacific, and they make up at least one quarter of all the coral species in the Great Barrier Reef. Their hard, carbonate structure forms the framework where other soft coral species, fish, and reef organisms can thrive, meaning the future of reef ecosystems are tied to the health of these reef-building coral species.

How can we conserve corals if we don’t accurately know which species grow where? 

“I like to think of staghorn corals like gum tree forests in southern Australia,” explains Bridge. “They’re everywhere, they provide all that habitat structure, and so they’re really important.

“While there may be a great diversity of other groups, like orchids or birds or insects living in the forests”, he continues, “many of those species couldn’t exist without the gum trees.”

Reef-building corals are declining around the world, with Staghorns being particularly susceptible to events such as thermal bleaching and crown-of-thorn predation. And there is rising concern that species of these and other coral groups will become extinct in the next few decades.

And yet, to date, techniques for identifying corals have been unable to confidently delineate Acropora species. The traditional technique of comparing morphological features of the corals’ calcium carbonate  skeleton, particularly against museum specimens, can be misleading; distantly related coral species may have very similar features, while closely related species can look very different, and sometimes morphology can also vary significantly within a single coral species, particularly when they occur in different habitats. So relying on this qualitative technique alone to identify coral species has proven problematic and confusing.

If coral species can’t be accurately identified, they are at high risk of ‘silent extinctions’ — lost without anyone even realising. Fortunately, Bridge recognised that molecular DNA methods to resolve the coral species’ conundrum already exist and have been widely used to examine the diversity and evolution of other animal species.

 “We [coral taxonomists] are still trying to identify species like we have since the 1980s — this is a different species because it looks different — and yet there are molecular methods for analysing complex genomic datasets,” explains Bridge.

“These molecular techniques are used to understand all sorts of questions, including our own [human] evolution,”  he continues, “So, really, it was a matter of applying what others have already done to corals.”

If coral species can’t be accurately identified, they are at high risk of ‘silent extinctions’.

By comparing DNA sequences Bridge and colleagues are applying a quantitative, data-driven approach that can be tested against other lines of evidence, like morphology.

In their most recent work, Bridge, with a team of international researchers, sampled an Acropora group containing the species A. tenius and its relatives across the Indo-Pacific, long presumed to be widespread from the South Pacific, to the western Indian Ocean, down to South Africa and north into the Red Sea.

Their DNA results, however, showed that A. tenius is not a single species spread across the Indo-Pacific but several distinct species of Acropora, each with smaller ranges and populations, with A. tenius actually restricted to a small region of the South Pacific. They also discovered two new, undescribed species: A. rongoi from the Cook Islands and French Polynesia in the South Pacific; and A. tenuissima, the specimen Bridge collected from the central Great Barrier Reef.

According to Bridge, these latest findings confirm what they have found previously.

“Every time we go somewhere and [DNA] sequence sampled corals, there’s new and undescribed species,” he says. “And species are more localised and in smaller populations than previously thought.”

And this has important implications for coral conservation. First, there is still much that we don’t know about which coral species grow where, even in the Great Barrier Reef.  Second, with smaller population sizes and geographic ranges, reef-building coral species are at greater risk of environmental threats and could potentially, for example, be wiped out by a single bleaching event.

But delineating coral species using molecular phylogenetics is just one part of the team’s work. Another key aspect is to apply the correct names to the species ‘type specimens’, designated when species are first described and stored in museums around the world. These type specimens act as the archetype for that species and are essential to ensuring that every scientist studying corals is on the same page.

Yet, most coral type specimens are decades, even centuries old and no longer contain any living tissue for viable DNA analysis, making it difficult to reliably identify which species a name actually belongs to. And because old museum specimens from the 18th and 19th century sea voyages were often collected as curiosities, even purchased upon the voyage’s return to Europe rather than collected by on-board naturalists, important information about where they came from is missing.

So solving the coral species’ conundrum is now requiring taxonomists to team up with historians to figure out where type specimens were originally collected in order to sample new, live coral tissue for DNA analysis.

“There’s a historical translation that is needed to connect the sea journeys to the coral [type specimen] descriptions,” explains Professor Koen Stapelbroek, a historian from James Cook University who has come onboard the project to help decipher type locations.

“The challenge comes,” Stapelbroek says, “when you have a journey in 1822, but a specimen book published in 1826 with a number of corals that may actually be combined from two journeys plus an existing collection.”

Dr Tom Bridge and Dr Peter Cowman sampling corals in the Great Barrier Reef. Credit: Project DIG, Queensland Museum

So Stapelbroek, together with Bridge and a team of historians, taxonomists and GIS experts are creating a global, digitised map of what these original sea voyages explored. By searching through historical texts and ship logs and asking broader questions, such as what were the different people on board looking for; what were their interests (scientific, political, economic); and how did those different interests add up to a general purpose or character of the expedition, they are assimilating data points of where sea voyages went and where they likely sampled type specimens. Those data points are translated into coloured lines of the journeys, thereby creating a visual research tool that Bridge and other taxonomists can use to determine where to dive next for type locations.

As they continue their work, it appears that refining our understanding of reef coral diversity isn’t just coming down to advanced phylogenetics.

Stapelbroek describes the process in historic terms: “It’s almost like a combination of state-of-the-art science and a bunch of medieval monks doing really old fashioned history, but then with a new research tool: global mapping.”

And as we begin to better understand which coral species grow where, perhaps a new page is turning for reef-building corals and their ecosystems, too.