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The first thing Captain Kenny McCain noticed at Seahorse Key was that something was wrong with the sky. It was a drizzly morning in April 2015, the first break in a freak spring squall that had lashed Florida’s Gulf Coast for two days. Captain Kenny, as he’s known around Cedar Key, the Big Bend fishing town where his family has lived for seven generations, had motored his skiff three miles to the outermost island of the Cedar Keys National Wildlife Refuge. He was planning to check on the facilities of the Seahorse Key Marine Laboratory, to see how the University of Florida research station had weathered the storm.

Captain Kenny knows the island better than most. After 24 years as an officer of the refuge, he left the U.S. Fish & Wildlife Service in 2014 to take up with the lab, shuttling students and scientists out to the wild, 165-acre island they shared with an alarmingly dense population of cottonmouth snakes and some 10,000 to 20,000 colonial nesting birds. He was a half-mile from the dock when he noticed something that made him change course: The skies above Seahorse were eerily empty.

Swinging his boat around to the island’s west side, he pulled in next to a mangrove-shrouded peninsula, typically the epicenter of the Seahorse Key rookery. He killed the motor and was stunned by silence. Two days earlier, the chatter of pelicans, cormorants, and maybe 10 different species of wading birds had been all but deafening. Now the only sound he heard was the rhythmic swoosh of waves against the beach.

When deputy refuge manager Larry Woodward answered his cell phone that afternoon, he recognized Captain Kenny’s drawl. “Got a problem out at Seahorse,” he heard Kenny say. “You ain’t got no birds out here.”

Predators. Parasites. Disease. Food-supply disruptions. There are a handful of perfectly prosaic reasons why colonial birds might call it quits on a spot where they’ve nested for decades. Colony abandonment, as biologists call it, is fairly commonplace, though it’s usually a gradual affair and rarely affects a wide swath of species at once, seeing as one bird’s precise habitat, prey, or foraging ground is often little more than scenery to its neighbor.

But then there are the Roanokes of the avian world: colony abandonments so massive, abrupt, and unexpected that they leave behind little more than empty nests and riddles. What kind of cataclysm prompts thousands of birds to leave a season’s worth of eggs they’ve invested tremendous energy into laying and incubating? How does so Vesuvian a disturbance escape our notice? What factors determine whether a colony ever returns—and if it doesn’t, what fallout awaits the ecosystem it’s left behind?

A few weeks after Captain Kenny’s visit, national media including NPR and The Rachel Maddow Show picked up the story of the mysterious abandonment at Seahorse Key, and managers at the Cedar Keys Wildlife Refuge suddenly found themselves bombarded with citizen theories: invasive pythons, magnetic anomalies, monitor lizards, underwaters methane gas bubbles . . . even black-ops government helicopters. “We heard all those and more,” says Woodward. “The best was the Russian submarine that was offshore testing a new sonic weapon. That was a guy from Texas who called in—he obviously doesn’t realize how shallow it is out there.”

“We couldn’t get a submarine within 10 miles of here,” Vic Doig, Cedar Keys’ fire-management officer and de facto wildlife biologist, says with a laugh. In the wake of the abandonment, though, people just wanted answers—however outlandish. “You couldn’t go anywhere in town where everyone wasn’t talking about it. They’d mob us: ‘What’s going on? Where did the birds go?’ ”

One sweltering afternoon in August, Doig and Woodward led a photographer and me out to Seahorse Key, searching for remnants of what was once the largest bird colony on Florida’s Gulf Coast. We tromped across a ribbon of golden-sand beach and into a swampy tangle of black mangroves, palms, cacti, and the occasional sprawling live oak. The ground was covered with crunchy palm fronds and, in the marshier spots, the thin, upward-pointing pencil roots of the mangroves, like spiky shag carpeting. Zipper spiders the size of baseballs clung to webs between trees, and Doig reminded us to keep our eyes peeled for the venomous (and potentially deadly) cottonmouths.

“This was ground zero,” he said, gesturing here and there at rickety remnants of nests scattered through the multi-story growth. Before the abandonment, he explained, seemingly every branch was occupied by Great Egrets, Great Blue Herons, Tricolored Herons, Snowy Egrets, Roseate Spoonbills, and other wading birds. Brown Pelicans and Double-crested Cormorants crowded the beaches. White Ibises, though less site faithful than their colony-mates, were often so plentiful that they took to nesting on cacti—although they were scarce around Seahorse that spring, which is either a clue or red herring, depending on whom you ask. Most nesting birds around Cedar Keys aren’t migratory; they simply follow good foraging around Florida and throughout the Gulf. And yet, while the colony’s numbers have fluctuated, the birds have reliably returned to Seahorse every March through August or so since at least the early 1900s.

Two days after Captain Kenny’s phone call, Doig arrived at Seahorse with a delegation of University of Florida biologists looking for answers. There wasn’t a straggler bird in sight, Doig remembers. The place was “empty, desolate, not a single bird, nothing.” It smelled too, a sulfuric stench from the tens of thousands of rotting eggs that littered the ground. The researchers wondered: Could predators have done this? The island’s cottonmouths have historically left birds alone, preferring to feed on fish scraps the birds drop, and they also keep the island’s rat population in check. Neighboring islands, though, have substantial numbers of raccoons sometimes known to swim over. Could a whole posse have invaded and terrorized the birds into fleeing?

Probably not, says wildlife ecologist Peter Frederick, one of the UF professors called to investigate. The eggs had been scavenged sometime after nests were abandoned, he explains—likely by Fish Crows, judging from the visible peck holes in the scattered eggs. Raccoons, by contrast, would have crushed them. What’s more, says Frederick, the Seahorse colony has weathered raccoon incursions for decades. The researchers saw little scat and just a few paw prints, and when they set traps on beaches where invasive raccoons tend to loiter, they caught none. “If there were a lot of raccoons out there,” he says, “we would have seen it.”

The investigators did turn up some 20 dead birds and one dead rat—an unremarkable number of carcasses for so big a rookery—and sent them off to two federal wildlife labs focused on forensics and pathology. Neither came back with any evidence of predation, parasites, or disease (though the rat, Woodward says, apparently had a hemorrhoid).

Once we’d seen our fill of skeletal nests, Woodward motored us a couple of miles east to another refuge island, called Snake Key, just 39 acres and equally jungly. Before the abandonment, it had hosted only a few nesting Tricolored Herons, but Doig estimates as many as a third of the birds from Seahorse resettled there in the days and weeks following the exodus in 2015. Nearly every species was represented, and many pulled off late broods. The fact that birds bred successfully so nearby suggests that they didn’t leave Seahorse for lack of food resources—a theory also undercut by the fact that varied diets across species make it an unlikely culprit, and no fisheries data suggest a food-supply crisis.

Which brings us back to those covert government helicopters. Maybe.

With so many natural disturbances seemingly ruled out, the refuge detectives considered human disturbance. Moderate man-on-bird harassment isn’t unheard of around the refuge, and Woodward and other officers have issued citations for things like illegal camping, boating, and fishing around Seahorse during its protective spring closure, even private helicopters landing on other refuge islands. “To get a whole colony abandoning because of human disturbance,” says Frederick, who’s ridden a clamorous airboat right up alongside rookeries in the Everglades, “you’d have to have something pretty large.”

Refuge officials have received unconfirmed reports from Cedar Key locals claiming to have seen, at great distance, one or more helicopters over Seahorse during the stormy nights before Captain Kenny’s discovery. Of course, they’ve also received reports of submarines. But the notion of government aircraft is less farfetched.

“Anyone who spends a fair bit of time out here by the water has seen military aircraft,” says Doig, who once had a screaming pair of A-10 jets interrupt a shorebird survey. Nearby Air Force bases fly maneuvers along the sparsely developed coast. More nefarious operators are drawn there, too, so Coast Guard, Homeland Security, and Drug Enforcement Administration operations aren’t uncommon. Of course, none of these agencies are inclined to reveal their flight plans, but Doig says the refuge staff, via unofficial interagency chatter, has reason to believe there was “aviation activity in the area that week.”

“The most likely scenario,” he says, stressing that it’s based on hearsay and speculation, “was that it happened at night, and the pilots would have been flying with night vision. So imagine 10,000 warm-blooded birds just lighting up the sky to some guy who works off infrared, who might have gone over to check it out. And then, yeah—all of a sudden they’d have just started coming up in waves and waves.”

But once a stubborn colony is sitting on eggs, even a Chinook full of rappelling paratroopers may not be enough to displace it—not by itself, anyway. Which is why Doig, Woodward, and Frederick all suspect a combination of factors at play on Seahorse Key: maybe some increased predation, some colony-wide jitters from the storms or lack of White Ibises, plus a traumatic visit from an aircraft. Stress in a colony is often cumulative, says Steve Kress, ����APP’s vice president for bird conservation and director of its Seabird Restoration Program. “People see, all of a sudden, a longstanding colony go away,” he says, “but they’re only seeing this final phase, and there’s probably been trouble there already.”

Dan Roby, a wildlife ecologist at Oregon State University and a scientist with the Oregon Cooperative Fish and Wildlife Research Unit, suspects cumulative disturbance is to blame for the mass abandonment of the world’s largest Double-crested Cormorant colony this past summer. In mid-May, somewhere in the span of three days, around 16,000 birds deserted eggs on East Sand Island, at the mouth of the Columbia River. “We couldn’t understand how something like this could happen,” says Roby, who has long been involved with research and monitoring on the island.

East Sand Island’s cormorants, however, are the targets of a controversial Army Corps of Engineers culling program, which seeks to more than halve the number of breeding pairs in order to protect salmon and steelhead smolts that cormorants feed upon. In 2015, federal wildlife officers shot more than 2,300 cormorants and oiled eggs in some 5,000 nests, a technique that prevents hatching by cutting the flow of oxygen through the shell. When researchers on Roby’s team alerted him to the abandonment, his early suspicion was that some righteous defender had motored out and loosed a sheepdog on the colony, preferring to see it abandoned than let any more birds get shot.

But neither the Corps’ investigators nor Roby’s colleagues monitoring terns on the other side of the island could find any evidence of humans or predators making landfall. The Corps points to more than a dozen Bald Eagles spotted lurking around the colony’s empty nests, but Roby thinks these were opportunistic scavengers. The simplest explanation fitting the evidence, he says, is that the cormorants were repelled by cumulative stress from the oiling (which flushes birds and invites egg-snatching gulls), the shootings (which result in mateless birds and failed breeding attempts), and the associated human presence.

“They got to some sort of disturbance threshold they couldn’t tolerate any longer,” Roby speculates, “and once large numbers started to abandon, basically the colony collapsed and everybody left.”

Particularly when multiple stressors are involved, there’s merit to the notion of a “tipping point,” says Kress—a certain number of birds that, once disturbed enough to flee, prompt the rest to up and join them out of something like peer pressure. It’s how Neil Shook, refuge manager at North Dakota’s Chase Lake National Wildlife Refuge, explains another Roanoke-style abandonment from more than a decade ago. In summer 2004, the refuge’s nesting colony of 30,000 American White Pelicans suddenly scattered, leaving behind eggs and chicks. It’s conjecture, Shook admits, but he suspects a combination of disturbances: a bad year for tiger salamanders (a key food source), a late cold snap, and coyote predation on a peninsular subset of the colony, whose panicked evacuation was enough to “scare up” the island-dwelling remainder.

Two years later Chase Lake’s pelicans came back in record numbers. This past July several thousand of East Sand Island’s displaced cormorants returned and laid second clutches of eggs. Down on the Gulf, meanwhile, Seahorse Key remained empty this year, despite Doig and Frederick’s efforts to seed the nesting grounds with decoys (a technique that’s been successful with some species of waterbirds).

The White Ibises, all but missing from the refuge in 2015, returned in greater numbers last spring, but they nested on Snake Key, which this year hosted some 6,000 to 8,000 birds, approaching half of what once settled on Seahorse. So given that most individual ibises weren’t actually around for the exodus, what’s keeping them from the excellent habitat at Seahorse?

“There’s both attraction and repulsion going on,” says Frederick. Seahorse evacuees that went to Snake last year will likely keep returning there, sticking with what worked the season before, and other birds will simply follow the leader, because that’s what colonial birds do. Doig suspects two new, small colonies north of the refuge also consist of former Seahorse birds, and each good season there helps overwrite whatever attraction they once had to their old nesting site. Some birds did occasionally roost on Seahorse this year, which seems like progress—last year, the biologists say, birds wouldn’t even fly over it.

“It’s something we might not give birds credit for, but their memory is very good,” says Kress. “What happens in one year at a particular place, they just remember it. And if it’s a bad experience, they’re not going to go back there.”

Not everyone around Cedar Key believes government helicopters spooked the birds. Not John McPherson, who’s on the board of the Friends of the Lower Suwannee and Cedar Keys National Wildlife Refuges. His theory? “We have a lot of boats that come in and anchor for the night,” he says. “Somebody on one of those had a pet monkey, and they couldn’t handle it anymore, so they thought, ‘We’ll just release it on the deserted island here!’ ” When I ask why the primate hasn’t been found, McPherson smiles tongue-in-cheekily. “Well, it’s a very evasive monkey.”

Not Barbara Maple, who for years ran the bird-focused travel company Tidewater Tours with her husband, Captain Doug Maple (currently vice president of Cedar Key’s ����APP chapter). Barbara points to a new sign the FWS put on the island in 2015, citing a piece of Old Florida lore about Pelican Island, a wildlife refuge on the state’s eastern coast. When that refuge opened in 1903, it’s said that none other than the ����APP erected a welcome sign; the pelicans skedaddled, returning only after the sign was removed.

And not Captain Kenny McCain, who brought us out for one more visit to Seahorse the day after we toured the island with Doig and Woodward. Captain Kenny doubts reports of helicopters and blames predation. In the weeks after abandonment, he says, he spotted two adult and three juvenile eagles cruising the island, and he trapped several raccoons—not on beaches where researchers were looking, but on the other end of the island, near the Seahorse Key Marine Laboratory. The thousands of ibis missing that spring, he thinks, made the colony extra vulnerable.

“You know how they like to nest in big colonies for protection?” asked the burly, bearded captain, standing at the helm of his boat. “I think they lost that. The rest were jittery, and something just triggered them—predator-prey stuff.”

With us was Coleman Sheehy III, then the marine laboratory’s associate director (since September, a professor of natural sciences at Santa Fe College in Gainesville). Sheehy says the only bigger mystery than what scared off the birds is what will happen to Seahorse without them. For 15 years he’s studied the relationship between the island’s birds and cottonmouths. He and several other researchers have a paper in the works exploring whether that relationship is mutualistic: the sloppy-feeding birds providing fish morsels for snakes, the hungry snakes loitering below the nests and thereby deterring raccoons. When Kenny first called him with news of the abandonment, Sheehy didn’t believe him.

“I was terrified this was going to be it for the snakes on Seahorse Key,” he says, “and the whole system we’ve been studying that’s so unique is going to be gone.”

In search of snakes, Sheehy led us on a beach walk while Captain Kenny hung back at the lab. (“Three things in the world I’m scared of,” he said, “and that’s my mama, my wife, and snakes, in about that order.”) Here and there, we watched Sheehy stroll into the trees and stir up leaf litter using a hooked pole called a stump ripper. But when an hour of searching uncovered zero snakes, he sighed. “A couple of years ago,” he said, “I could have turned over just a few fronds and found you one.”

Daytime isn’t ideal for spotting nocturnal cottonmouths, but even Sheehy’s nighttime surveys suggest snakes are hurting on Seahorse—along a transect where he once commonly found 30 snakes a night, he’s now lucky to count 10. In fact, after two birdless seasons, Seahorse’s predator-prey dynamic is getting biblically weird: The cottonmouths are eating each other for lack of food. Long accustomed to their piscine meal ticket, Seahorse’s snakes tend to be both larger than their mainland counterparts (some more than five feet long) and more docile. The island has some rats, skinks, and squirrels, but the snakes aren’t great at catching them; consequently, Sheehy has found fewer and skinnier snakes this year, with two documented incidents of snake-on-snake cannibalism. 

Suddenly, Sheehy gave a little cry and dropped to his knees. “Wow!” he exclaimed, frantically placing his cupped hands over divots in the dirt where I saw only the tiniest blur of movement. Then he stood, triumphantly holding a slender, four-inch lizard with a chrome-ish back and a bright amber tail. A Cedar Key mole skink, he said, unique to these islands. Before releasing it, he handed it to me and said proudly, “You’re now one of the few people ever to have held this species.”

As much as he hates to see Seahorse’s snake population crash, Sheehy expects Snake Key’s small resident population will surge, now that birds have begun nesting there. And he’s excited to witness a transitional shift, to realize with each post-abandonment year new ways that the birds have shaped the island’s ecology—for example, through the huge nutrient influx of their guano. He gestured at the tiny tracks left by the retreating skink. “The food web here is complex,” he said, “and that’s just one species that has potentially, either directly or indirectly, benefited from the birds.”

Whether and how other species are impacted depends, of course, on how long the birds stay gone. And trying to predict that is like searching for a phantom evasive monkey. As we motored back to town, passing by Snake Key, Captain Kenny mentioned that the island once hosted its own thriving rookery. The birds gradually stopped nesting there in the early 1950s, he said. Again, no one really knows why.

“Just nature doing its thing,” Captain Kenny said. “So it’s been, what, 70 years? Maybe we’ll leave notes for our grand-youngins in 70 years and have them see if the birds come back to Seahorse.”