They thought the expedition was lost. Then, they spotted a whale almost no one has seen

When the engine of the research ship Pacific Storm broke down last month 400 kilometers off the coast of Oregon, it didn’t seem like a turn of good fortune. But the mishap, which forced researchers back to port for several weeks for repairs, ended up enabling the team to solve a mystery that has baffled marine biologists for years.

Once the scientists were able to again set sail, they found themselves battling 3-meter waves and wind gusts reaching 40 kilometers per hour. But the rough conditions didn’t prevent them from standing, transfixed, after two beaked whales—reclusive, deep-diving marine mammals known for their long, dolphin-like snouts—appeared nearby and started frolicking.

The 23 September encounter marked one of the few times scientists were able to observe this rarely seen species in the wild. More importantly, it also allowed them to answer a question pondered by a handful of people who listen for whale sounds in the deep ocean: Who the heck was making a series of distinctive chirps so high-pitched they defy human hearing?

The episode “still is unbelievable to me,” says Lisa Ballance, a marine ecologist at the Oregon State University (OSU) Marine Mammal Institute, who led the trip. “I call it pulling a scientific rabbit out of a hat.”

Though beaked whales can grow to the length of a pickup truck and outweigh a Clydesdale, they remain largely invisible. Scientists don’t even know how many species there are. The size of their populations, the extent of their habitat, and exactly what they eat are all mysteries. Even marine mammal specialists can have a hard time telling some species of beaked whales apart—when they get to see them at all.

“It’s just amazing to me to think that here’s a really big animal floating around on our planet, and nobody’s ever looked at one and said, ‘Oh, I know what that is,’” says Robert Pitman, a marine mammal biologist retired from the National Oceanic and Atmospheric Administration (NOAA) who was part of the expedition.

Pitman has set his eyes on 85 of 93 known whale species and aspires to complete the list. Six of the eight species he hasn’t seen are beaked whales. Call them the Moby Dick to his Ahab.

Beaked whales are rarely spotted because they spend their lives largely in the open ocean, far from shore, diving more than 1000 meters deep to feed, probably on squid and fish. Their elusive behavior might, in part, represent a way to avoid killer whales, which prey on them. Beaked whales also remain largely silent until they are deep enough to avoid their black-and-white cousins, surfacing infrequently to refill their lungs.

Much of what’s known about this whale family comes from dead beaked whales that wash ashore. But the emergence of genetic testing and underwater listening devices has begun to shed more light on the animals. DNA enables scientists to figure out when they have found a new species. And microphone-wielding researchers have learned over the past decade that many beaked whale species emit distinctive chirps used for echolocation while hunting prey in the dark depths.

Marine biologists have amassed a catalog of more than 20 such hunting sounds, and they’ve been able to connect a dozen calls to the species that make them. That leaves more than 10 unclaimed calls—either because a known species hasn’t been clearly linked to a sound, or because it’s from an unknown beaked whale.

To help fill the gaps, a team of scientists from OSU and NOAA motored out of Newport, Oregon in early September, bound for the Great Pacific Garbage Patch, a section of the northern Pacific Ocean where currents concentrate plastic trash. Someone studying the plastic had reported seeing a beaked whale that might be a new species. The Pacific Storm boasted high-powered binoculars for scanning the horizon, a waterproof microphone tethered to the ship by a 100-meter cable, and a room packed with acoustic equipment for analyzing sounds picked up by the microphone.

But the expedition foundered on day three, with the ship struggling to stay in gear after its transmission malfunctioned. The boat limped home. After repairs, the team decided to spend their remaining time cruising along undersea mountains closer to the Oregon coast.

That’s when someone running the listening station reported the trademark sounds of a beaked whale followed by silence—a sign that the animals might be swimming to the surface.

On deck, Ballance and others scanned the waters for more than 1 hour before she spotted two whales surfacing just 400 meters from the ship.

The whales put on an unusual display for the next half-hour. They swam close to the boat and surfaced as the researchers filmed and shot hundreds of photos. At one point the animals drew close enough that Pitman, armed with a crossbow, fired a special arrow into the back of one of the animals. The arrowhead jabbed out a plug of blubber the size of a pencil eraser, then fell out, drifting until the crew caught it in a net.

The researchers weren’t sure what kind of beaked whale they were watching. (Juveniles and females are especially hard to identify.) But back at the Newport lab, DNA taken from the tissue sample revealed what their observations and photos couldn’t: One of the visitors was a female Hubbs’ whale (Mesoplodon carlhubbsi), first identified in 1945—though it was mistakenly lumped with another species at first—and rarely observed since.

The DNA results also enabled the researchers to identify the song of the Hubbs’ whale. The chirps heard aboard the ship matched a sound sample previously known just as BW37V, which stands for “beaked whale” with the valley (V) between two chirps registering at 37 kilohertz. (Human hearing tops out at about 20 kilohertz.)

Not all such whale hunts are so successful. Simone Baumann-Pickering, an acoustic ecologist at the University of California, San Diego, first described how sounds could be used to distinguish beaked whale species in 2013. She was recently part of an effort to pinpoint the origin of nighttime beaked whale sounds recorded near the Hawaiian islands. She suspects it’s the gingko-toothed beaked whale (M. ginkgodens), because they have been spotted in the area.

But the whales went silent during the day, making it hard to link them to the sounds. In early mornings, a crew would speed to an area where the whale sounds had occurred overnight, hoping to find whale DNA floating in the water. No luck. “That mystery keeps on giving,” Baumann-Pickering says.

New types of underwater microphones that could be attached to all kinds of vessels—including cargo ships and recreational boats—could soon make it easier than ever to track beaked whales, says NOAA researcher Jay Barlow, who specializes in acoustic tracking of marine mammals and took part in the Oregon trip. “This will be a tremendous step forward in looking at places like the middle of the ocean, where a lot of research vessels never go,” he says. It should also make it easier to learn more about some of the planet’s most furtive and enigmatic whales.