Portions of the once vibrant reef ringing the South Pacific island of Mo‘orea are now an apocalyptic landscape of gray rubble. Under the rich turquoise-colored surface, dead coral towers lie in pieces, blanketed with a fine layer of decay.

What has caused such trouble in paradise? A nasty invasion of armored starfish. The crown of thorns (Acanthaster planci or taramea in Tahitian), with menacing poisonous spikes and a voracious appetite, literally sucks the life out of reef communities. The starfish feast on coral polyps, leaving an empty white skeleton and ransacked home for other marine species before moving on to the next meal.

But thanks to unique research on this island just 12 miles (20 kilometers) northwest of Tahiti, scientists may be able to predict outbreaks like the crown-of-thorn siege. In fact, Mo‘orea could eventually serve as a model for understanding how ecosystems respond to stresses such as invasive species, climate change, and pollution.

One key is ambitious scientific research called the Biocode Project—a four-year, $5 million effort to collect, document, and genetically sequence the non-microbial biodiversity of the island. When the project wraps up this year, it will be the first time a complex tropical ecosystem has been catalogued in such detail. Biocode scientists have come from around the world to find and “barcode” the species they specialize in—from fungi, snails, insects and plants, to algae, crabs, marine worms, and coral. DNA bar coding uses genetic markers to identify species and offers a simple, standardized way to analyze lifecycles and interactions.

“The goal is to build a catalogue of digital signatures,” explains Chris Meyer, a zoologist and curator at the Smithsonian Institution. Meyer directs the Biocode Project, which will enable other scientists to more efficiently identify species, better understand how they behave and interact, and recognize how many species may actually be at risk.

“Ultimately, we want to answer the question: how much biodiversity is needed to ensure ecosystems continue to function?” says Neil Davies, Biocode’s principal investigator. “It should be clear that this is a difficult question to answer if you don’t know how much biodiversity you have in the first place.”

DNA on Ice

Mo‘orea is smaller than the District of Columbia, but it’s home to two prodigious research stations—University of California Berkeley’s 25-year-old Gump Station, and the 40-year-old Insular Research Center and Environmental Observatory (CRIOBE) a joint venture of France’s National Center for Scientific Research and School of Advanced Studies. Working in concert, scientists on the island have already collected more than 37,000 specimens, from which 251 algal species, 200 fungal species, 3,000 marine invertebrate species, 600 marine vertebrate species, 930 plant species, 700 terrestrial invertebrate species, and 21 terrestrial vertebrate species have emerged, so far.

View Images Illustration by Stephen Rountree

Meyer has spent countless hours sifting through the reef with a wide variety of sampling methods—plankton nets, baited traps, automated reef monitoring structures, vacuums—and now picking through the rubble by hand. He estimates that at least 30 percent of the marine species they’ve found are new to science.

Tissue and DNA have been extracted from every specimen. Some of the sample is shipped to universities and museums, and the remainder is stored at Gump. “The entire island is in there,” Meyer says as he points to a six-by-three-by-two-foot freezer, which looks like the kind you keep in your basement full of extra summer berries and frozen fish but is actually -112 degrees Fahrenheit (-80 degrees Celsius).

Why Mo‘orea?

With its forests, lagoons, reefs, and freshwater and marine habitats, Mo‘orea is a typical tropical island, but located toward the eastern end of a natural biodiversity gradient across the South Pacific, and so isn’t overwhelmingly diverse like some western Pacific islands. That’s one reason it is an ideal ecosystem for creating a comprehensive genetic catalogue of species. Biocode is, in some ways, keeping it simple.

The island also is unique in that it now has sophisticated research facilities to complement its tradition of hosting international scientists. Along with that tradition comes a long-term record of the island’s ecological trends.

Forty years ago, a French foundation wanted to send an expedition to the Pacific to study reefs, explains Serge Planes, the French scientist who directs CRIOBE and leads the Biocode team specializing in fish. “That was at the exact time army forces from France started nuclear atoll testing” on the neighboring Tuamotu archipelago, he adds. The scientific outpost was never an official monitoring effort for nuclear testing, explains Planes, but it did pave the road for researchers to come to Mo‘orea.

“Biocode is intended to help develop Mo‘orea as a model ecosystem for environmental research, as the fruit fly or mouse is a model species for biomedical research,” Davies explains. “Model species were the first to have their ‘whole genomes sequenced.’ We want Mo‘orea to be the first ‘whole ecome sequenced’.”

Biocode in Action

Meyer, Planes, and Davies hope the Biocode digital library of genetic barcodes, available to the public, will not only aid other scientists, but also establish Mo‘orea as the testing ground for new technologies in monitoring ecosystems and studying how species interact with each other.

Davies, whose expertise is the genetics of biological invasion, points out that being able to map genes across an entire ecosystem enables scientists to trace and mathematically analyze interactions among Mo‘orea’s species. “For example,” he explains, “food webs reveal energy flows through a system, and network theory provides one way of studying how resilient different systems are to change. We then need real-world observations and experiments to test and refine our theories. Post-Biocode Mo‘orea is a place where we can begin to do this at an appropriate scale: the whole ecosystem.”

Biocode, which is supported by a grant from the Gordon and Betty Moore Foundation, shares the Gump station with the Mo‘orea Coral Reef Long Term Ecological Research (LTER) program. Funded by the National Science Foundation, the Mo‘orea LTER was established in 2004 to determine how the reef will respond to short- and long-term disturbances, and its scientists think the Biocode data could help them better understand the interaction between fish and coral.

For instance, damselfish fertilize the reef with their waste products, and in turn, the corals provide shelter for the fish. But both the coral and the damselfish eat zooplankton. If they are competing for the same species of zooplankton, that symbiotic relationship could be harmed. The problem up until now is that “if you look at much of what’s in a coral’s stomach, or a fish’s stomach, animals that feed on things like zooplankton, the stomach contents looks like oatmeal . . . it is impossible to tell the exact species,” says Andrew Brooks, deputy program director of the Mo‘orea LTER.

But Biocode data would allow scientists to examine the stomach contents and tell if the coral and fish are vying for the same food source. “That is a major advance,” Brooks adds. “Biocode gives you a way to identify the pieces. We put what Biocode does in context.”

With continued monitoring and sampling, the Biocode database may also allow scientists to better understand biological disturbances, whether that’s crown of thorns or an invasive plant, by identifying previously unidentifiable larvae in the water, or seeds in the soil, before they grow up to become an invasion, Meyer explains. “It allows us to use these digital signatures to see things that aren’t established yet,” he adds.

Biocode data “give us a brand new tool to address why coral reefs behave the way they do,” says Russell Schmitt, lead principal investigator for the Mo‘orea LTER. “We’re just beginning to discover the tremendous opportunities it provides.”

Reef Recovery

As for the starfish-devastated parts of the reef, scientists say they think the coral will come back. Growing populations of herbivorous fish ar­­e eating algae off the dead coral, suggesting that the system won’t remain in an algal state like other crushed reefs that have not fully recovered. “Herbivorous fish are going like gangbusters, and that’s a good sign,” Meyer explains. “Moreover there are plenty of smaller animals still living within the nooks and crannies of the reef.”

If you ask island elders, and scientists like Planes who have been on Mo‘orea for a while, they will tell you that a crown-of-thorns invasion happens every 20 years or so. Stories of the starfish creeping over the reef shelf and into the lagoon are part of anci­ent island chants. Similar patterns have been recorded in Australia and elsewhere. Recovery can take more than a decade, Planes says.

The chances of recovery this time are muddied by new challenges—climate change, coral bleaching from increasing water temperatures, ocean acidification, and land use changes on Mo‘orea that could load lagoons with nutrient-rich sediments that affects fish nursery productivity. To add insult to injury, Mo‘orea’s north shore, where the starfish had their fill, was hit by Cyclone Oli in 2010, which turned much of the dead coral into rubble.

“In 2006 dead coral heads were hard to find,” Meyer says. “Now it’s ‘How many do you want?’ ” In less then four years the outer reef of the north shore went from as alive as it gets to between 2 and 5 percent live coral.

Adds Davies: “We did Biocode over a very tumultuous four years.”