For more than 200,000 years, staghorn corals were among the most common coral species in the Caribbean and western Atlantic, their natural range. In recent decades, though, up to 98 percent of staghorn coral colonies have died in this region. Like other corals here and worldwide, they’ve succumbed to disease, changes caused by climate change, declining water quality, damage from certain fishing practices, and other pressures. These are ongoing problems and the effects of climate change are becoming worse as shallow seas overheat more frequently. That has created particularly deadly conditions for corals in Florida and other Caribbean locations this past year. Yet somehow, staghorn corals survive at this unassuming reef known as Coral Gardens, an ecosystem awash in sundrenched water just a short boat ride from the bustling town of San Pedro, Belize.

Coral Gardens is what’s called a patch reef—an isolated area of corals that grow in quiet water sheltered from waves—and is just one of the many reefs that make up the Mesoamerican Barrier Reef, the second largest barrier reef in the world. For Lisa Greer, a geologist at Washington and Lee University in Lexington, Virginia, Coral Gardens is also a beacon of hope.

“We’ve spent far too much time documenting things dying,” says Greer. She’d like to understand why this reef is living. To that end, Greer has come to Belize each year—typically in June and December—since 2011 to monitor Coral Gardens, often with Macalester College geologist Karl Wirth, Smith College professor emeritus Al Curran, and a rotating cast of other scientists and undergrads.

Now, in December 2022, Greer, Wirth, and I swim through shallow, 82-degree water, toting measuring tools, notebooks, and cameras. Over several days, we’ll photograph about 140 square meters of coral. Greer and boat captain Narciso Valdez will swap out monitoring instruments that are tucked into the reef. Curran and his spouse Jane Curran will snorkel above for a broad perspective on what’s changed. And Wirth, clipboard in hand, will identify which species of fish dart in and out of the staghorn branches at certain spots within Coral Gardens—a task that requires the same stillness and patience as birdwatching.

The scientists hope that monitoring the reef’s health and analyzing environmental data from the site will help them understand what factors allow corals to thrive in this particular spot—and whether their resilience could help save other reefs.

When scuba equipment first became widely available in the mid-20th century, divers found vast thickets of staghorn coral in Caribbean reefs, branches golden-hued with life as far as the eye could see. But within a few decades, that changed. The species started to die in the 1960s, leaving drab skeletons behind. This was one in a series of coral casualties. Closely-related elkhorn coral (Acropora palmata), the other prominent Acropora species in the Caribbean, had started to decline a decade earlier. According to historical ecologist Katie Cramer, both may have been affected by a drop in water quality caused as booming human populations and newly-developed chemical fertilizers caused nutrient levels in water to spike with additions of sewage and agricultural runoff.

Then, in the mid-1970s, researchers discovered that the once colorful polyps of Caribbean Acropora corals were peeling away, exposing their pale skeletons—evidence of white band disease, which increased the rate of Acropora decline. In the 1980s, coral bleaching began to spread through the region as climate change increased ocean temperatures, causing corals of many species to expel the algae that live symbiotically within their bodies. Corals rely on the sugars these algae make through photosynthesis, so bleaching leaves them weak and often without enough food to survive. Some bleached corals recover once water temperatures return to normal enabling them to regain their algae. Some die before waters cool. There’s evidence that heat has made white band disease more deadly, as well.

Today, the International Union for Conservation of Nature lists staghorn coral as critically endangered, the most grave designation for a species that still exists in the wild. Caribbean reefs have suffered declines of many species, but staghorn coral has been among the hardest hit. Now only small and isolated populations remain, although in some Caribbean reefs, like Dairy Bull Reef in Jamaica, there are signs that staghorn coral is returning. There, tumbleweed-shaped thickets now grow atop the skeletons of corals that died decades ago. And a hybrid between the two Acropora species, known as Acropora prolifera, is flourishing on some Caribbean reefs, a sign that it may be better able to cope with the barrage of threats to coral health than its parents.

A couple of years after Greer’s first visit to Coral Gardens, she and her team began studying the reef’s underlying structure to understand whether the thriving staghorn corals were bouncing back after the struggles of the 20th century or whether they had lived through those difficult times. The skeletons of coral ancestors typically lie below the living surface of a reef, making it possible for scientists to assess its history based on its layers of growth. During the decades when staghorn colonies were dying throughout the Caribbean, Greer’s team found no major breaks of growth at Coral Gardens—no evidence that the staghorn corals had been decimated. In fact, staghorn corals there appeared to have grown more or less continuously for over a century, according to age dating by University of Wollongong (Australia) geochemist and paleoecologist Tara Clark. The Coral Gardens reef appeared to be serving as what scientists call a refugium.

Refugia are places that shelter species through times of climactic upheaval or other environmental change. Much like Covid lockdown in a small apartment, refugia typically offer conditions that are just livable, not ideal. For corals, ideal conditions include water that’s neither too hot nor too cold, low levels of pollution and disease, plentiful fish to graze away algae that can otherwise outcompete corals for space, and predators that keep grazing fish populations in check. But a refugium may be small and isolated and some conditions may not be ideal, making life more challenging for corals. Refugia may also be spots where corals have increased ability to survive challenging conditions.

During the last Ice Age, such places helped reef life make it through wild fluctuations in sea level. Now, scientists are searching the tropics for refugia that may serve a similar role as global warming marches onward.

Floating above the largest thicket of staghorn at Coral Gardens, it’s easy to conclude that nearly all of it is alive. In reality, though, very few reefs—here or elsewhere—are entirely covered with live coral. Estimating the percentage of living coral and tracking how it changes over time is the next step in Greer’s effort to estimate this particular patch’s chances of surviving into the future.

Breathing from the tank on her back, Greer unwinds a tape measure as she swims over the reef, laying a transect line along which the team can collect data. Then, she frames each square meter of reef along the tape with a square of PVC pipe. Wirth swims above to take a photo of each plot as she moves. Then I take the same photo as a backup. After they’ve collected data along five transect lines, the team will digitally trace the live coral in each image, calculating the percentage that is alive. They’ve repeated this process at least annually for 11 years.

So far, the data suggest that although this reef’s staghorn coral is persistent, it’s not invincible. Between 2016 and 2017, Coral Gardens lost nearly half of its living staghorn coral. The largest thicket suffered the largest loss. When Greer’s team started monitoring it in 2012, living coral cover there was over 50 percent—similar to the proportion of live corals on healthy Caribbean reefs decades ago. But by 2017, the number had dropped to just 18 percent, about average for a Belize reef today.

Two instruments nestled within the reef, each about the size of a Tic Tac box, have helped explain why. Lightly encrusted with limestone and algae, each small plastic container holds electronics that have been recording water temperature every hour of every day since 2012. The data show that 2016 was abnormally warm, and stayed warm for an abnormally long time, due to the one-two punch of El Niño and climate change. While El Niño is a natural cycle, when combined with climate change, tropical oceans heat up far more than usual—a phenomenon that has now reappeared in 2023, sending reefs into hot water and causing widespread coral bleaching in the Caribbean this summer.

The corals endured yet another blow when, after more than two months of heat stress in 2016, Hurricane Earl made landfall in Belize on August 4 of that year, felling trees and scattering debris from damaged buildings across San Pedro. The researchers found that staghorn corals continued to die off after the storm. Only a few colonies were broken or overturned by the storm’s waves, but waves can also cause a flurry of sediment which the researchers suspect may have been lifted up from the seafloor, causing harm to corals by abrading coral polyps or smothering them with sand grains. Given the reef’s location far from shore and river outlets, they think it’s unlikely that sediment was carried into the reef from coastal runoff. Greer and her team found no evidence that storms over the past century caused the corals to die. They believe that Hurricane Earl may have added insult to injury—many corals, already weakened by heat stress, could not survive the storm.

Yet there’s hope that staghorn corals in this particular place may have a special ability to bounce back. Since the 2016 decline, the amount of living cover stabilized and eventually started to increase in some areas. In 2019, the largest staghorn thicket had jumped up to 25 percent live coral cover. By 2022, when I follow the team collecting data on the reef, there is 35 to 40 percent live coral—a near-complete recovery. This occurred even as other coral species on the reef, like brain coral (mainly species of Pseudodiploria) and star coral (Orbicella species) have bleached. That suggests that the staghorn didn’t simply recover because environmental conditions improved. Something else appears to be going on—perhaps a genetic advantage or an ability to acclimate to warmer water. Recent research has found that there are a number of different ways that corals—at least some species—may be able to increase their resilience to heat. This can include adaptation over many generations, which passes on beneficial genes. Corals are also known to adjust their gene expression or swap their symbiotic algae for a heartier variety. At Coral Gardens, it’s unclear what gives the staghorn coral the ability to bounce back. “It is under threat,” Greer says. “But it still is remaining somewhat resilient.”

Forman-Castillo’s team transported all the fragments in buckets of seawater to protected, shallow waters just south of the reserve’s namesake channel through the barrier reef —“hol chan” is Mayan for “little channel.” There, they’ve created a coral “nursery”—a place where the fragments can grow safely. When waves break corals, the surviving pieces can naturally form new colonies; reef restoration projects like this one are now capitalizing on this innate ability at sites around the world. Experts say that reef restoration is an effective strategy to help the ecosystem survive this century, along with efforts to address the causes of climate change and reduce pollution.

Greer pulls up the anchor and Valdez takes us about two miles northeast of Coral Gardens to see what Forman-Castillo and her team have been up to. We find the coral nursery in a calm, turquoise sea. It looks like an underwater table, about 10 feet across, with its metal legs anchored into a seagrass bed. Most of the “tabletop” is made of rope strung across a metal frame at foot-wide intervals. Forman-Castillo and her team had previously tucked the small fragments of staghorn coral from Coral Gardens and elsewhere between each twisted strand, suspended above the seafloor like acrobats on a tightrope. Now, six months later, the little corals are growing branches in all directions. A nurse shark often loiters under the table; Forman-Castillo jokes that the shark works as nursery security.

In a year, she explains, the staghorn corals will fill the ropes like garlands of tinsel. Then, the team from Hol Chan will carefully remove each rope and tack it to dead coral skeletons in the reef beyond. In their new home, the corals will continue to grow, eventually cementing themselves to the reef’s limestone framework of dead corals, hopefully becoming a human-built refugium over time. The batch we’re looking at is the second to grow in the nursery; the first already lives on the reef alongside a few small surviving colonies. The transplanted nursery colonies are now up to two feet across and seem to be thriving in their new home.

Yet while they’re relatively small, these corals aren’t babies. In fact, they’re quite old. Because they are from fragments of mature corals, they carry the genes of colonies that have lived for decades or even centuries. Colonies with the same genes are called a genet. A survey of Acropora colonies in northern Belize estimated that the region’s oldest staghorn coral genet is more than 400 years old. The youngest was 62 years old. Given their age, these northern Belize genets all survived the stresses that killed other corals in recent decades—a good sign that they have the ability to persist through challenging conditions. They could even survive thousands of years into the future; the oldest known Acropora genets, found in Florida, have been around for over 5,000 years.

Staghorn coral is a favorite for reef restoration in the Caribbean both because it creates superb fish habitat and because it grows comparatively quickly, adding three to 11 centimeters to its branches each year. But including other coral species is important for boosting reef diversity. And adding corals that have more robust limestone skeletons may also help reefs keep up with sea level rise, building upward fast enough to remain within the shallow, sundrenched depths that corals require. Scientists have developed a new technique called microfragmentation that speeds up the growth of other species for restoration projects. Using a saw, researchers cut small slices from coral colonies, often no more than a centimeter wide, which stimulates tissue growth, and produces new clones at a faster rate. Unfortunately, many projects have put microfragmentation efforts on hold as Stony Coral Tissue Loss Disease (SCTLD), which attacks many slower growing species, spreads through the Caribbean. The disease was first identified in Florida in 2014 and spotted near San Pedro in 2020.

The restoration effort at Hol Chan Marine Reserve is one of many projects aiming to increase live coral coverage on Belize reefs. Fragments of Hope has trained about 90 Belizean coral restoration experts and employs many of them to care for corals in nurseries and monitor restoration sites. As of 2022, they’ve grown about 170,000 corals in 28 nurseries throughout coastal Belize. They’ve planted those corals into more than 17 restored reef sites in seven marine protected areas. Eighty-two percent of the first corals added to restored reefs survived and, over the years, these colonies have expanded to cover 60 to 70 percent of the restoration areas.

After scoping out the coral nursery, Greer, Wirth, and I meet Lisa Carne and several of her colleagues from Fragments of Hope at the nonprofit’s first restored reef, about 100 miles south of Hol Chan Marine Reserve, at Laughing Bird Caye National Park.

Crowded with corals and bustling with fish, the reef offers a vision of what Hol Chan’s restored reef could become in a decade or so. In the years since Fragments of Hope added nursery-grown corals to the site, they have continued to grow wild. Snorkeling through shallow water above the thickets, they look much like the natural reef at Coral Gardens. In some spots, their living tangle of branches forms a mosaic of amber hues across the seafloor. In other spots, the pale lumpy skeletons of dead corals peek through the living—the only evidence that this reef hasn’t always thrived.

To ensure that exchange, Fragments of Hope has filled the shallow water around Laughing Bird Caye with 17 genets of staghorn coral, 30 genets of elkhorn coral, and three genets of hybrid Acropora. As a result of spawning, there may now be new genets at the reef. From the edge of Laughing Bird Caye, Carne looks out at the reef offshore and wonders, hopefully, whether new coral offspring are out there with the traits they’ll need to survive in a changing world.

WWF has helped support Fragments of Hope since 2009, and over that time Nadia Bood has watched the benefits of Belize’s restored reefs extend beyond corals to other creatures too. “Those restored sites have biodiversity coming in,” she says. “You can see different species of fish and crustaceans in those sites. Even at the nursery tables, you can see different organisms recruiting to the tables and using [space] underneath the table as habitat as well.” Even before their charges are moved to the reefs, the nurseries take on a life of their own.

As we snorkel the reef near Laughing Bird Caye, we see plenty of evidence of the biodiversity Bood referred to. There’s a tiny juvenile monochrome drum fish that flits back and forth below an overhang of coral, its long dorsal and tail fins waving like ribbons. Large schools of grunts, parrotfish, and other grazing fish flow over the corals in glimmering formation. The water crackles with the sounds of their eating, and of shrimp snapping their claws.

Carne introduces us to a small bright blue fish—the endangered Maya hamlet (Hypoplectrus maya), found only in shallow waters off coastal Belize. Once I know what a Maya hamlet is, I start to notice them throughout the restored reef. Most loiter solo, each next to a thicket of coral, their azure color perfectly complementing the corals’ honey-hued symbiotic algae. These corals—artificially planted and tended by people—now shelter multiple species.

Will refugia like this one be enough to save staghorn coral and other reef species from extinction? If seawater becomes too hot, most are likely to fail. Models predict that Australia’s Great Barrier Reef will lose many of its pockets of safety if the climate warms beyond three degrees Celsius. But if humans finally manage to reduce their greenhouse gas emissions enough to limit climate change, and resilient corals manage to persist, it’s possible these sanctuaries will be able to shepherd reef life safely into the uncertain future. Perhaps, hopefully, corals can one day spread beyond their refuges again, and even thrive, as they have in the not-too-distant past.