TWELVE MILES OFF PROVINCETOWN — The dark waters began to roil. Silently, two black, 70-ton leviathans emerged from the depths of Cape Cod Bay, skimmed the surface, then quickly slipped back into the sea. Scientists in a nearby boat tracked their “fluke prints” — the large surface swirls created from their underwater tail sweeps — but soon lost the watery trail of two of the world’s rarest whales.
For years, scientists have sounded a dirge for the North Atlantic right whale. Its population stalled around 300 in the 1990s, pushing some researchers to make mournful extinction predictions for the mysterious, 45-foot-long creatures that come to feed and frolic every spring off Cape Cod.
Now, the critically endangered population has hit 500 whales, probably for the first time in centuries — a poignant milestone for a marine mammal whose numbers dwindled to perhaps a few dozen after being hunted relentlessly for their oil and baleen from the 11th to the early 20th centuries. Researchers, while joyful, say that number is still tiny — and they remain deeply concerned about recent environmental changes, including global warming, that spell uncertainty for the creatures’ future.
“Five hundred whales make you want to sing,’’ said Charles “Stormy” Mayo, senior scientist at the Provincetown Center for Coastal Studies, which studies the whales. “But you have to hold your breath when you sing. We have a substantially changing ocean. We don’t know what the future holds.”
Last Monday, he and his staff aboard the research vessel Shearwater scanned the horizon for spouts from the whales’ blowholes. An airplane flew transects above, searching for dark shadows in the relatively small bay and radioing their locations to the boat.
Scientists don’t know what a healthy right whale population even looks like, but they suspect it is in the thousands or even tens of thousands. Today, the population is increasing about 2.5 percent a year — far better than the 1990s — but hardly the 6 or 7 percent researchers would like to see.
The reasons for the increase are likely myriad. Ships have slowed down and moved to avoid the creatures. Fishing lines have been developed that allow some whales to avoid being tangled. A number of good feeding years — the animals can consume tiny shrimplike plankton at a rate of 125 pounds an hour — probably helped with a dramatic increase in calves starting around 2001.
“We have built up a reserve . . . a buffer,’’ said Philip Hamilton, a research scientist with the New England Aquarium, which also studies the whales. He expects the population to decline again, but says the whales will be able to weather a hit better with larger numbers.
Once, hunters’ harpoons easily found the right whale, so named because they were the “right” whale to chase. Lumbering through the water and often feeding close to the ocean surface, they floated when they died — making it easy for hunters to tow them to shore to collect oozing oil from their blubber for lamps, and baleen from their jaws to make items ranging from combs to corsets.
In 1935, the League of Nations outlawed right whale hunting, but by then, few whales were left. Unlike fishing stocks that often rebound once fishermen stop fishing them, the Northern right whale never regained a footing once hunting ceased.
Because the whales are studied so intensely and there are so few of them, researchers can identify most members of the population by sight through distinctive whitened skin patches on their gigantic heads. In Mayo’s Provincetown lab, a wall is lined with whale diagrams and identifying numbers, often with accompanying nicknames such as Legato and Monarch. Researchers have tried virtually everything to understand the whales — including training dogs to sniff out their orange scat at sea to better understand their hormonal processes, their diseases, and what they eat.
In efforts to protect right whales, all boats must stay at least 500 yards away from them unless they have a scientific permit to study them, or risk a $10,000 fine.
Nonetheless, the gregarious and outgoing creatures often put on shows close to shore that delight beachgoers with their feeding, socializing, and breaching. Groups of right whales sometimes feed close to the beach between Race Point and Long Point in Provincetown.
Now, the animals are showing up in larger numbers in Cape Cod Bay — far more than can be explained by the population increase — and they are showing up earlier.
In 2012, whales began appearing in early December, the earliest in 30 years. They usually start appearing mid-January to May.
In 2011, around 200 were spotted in the bay, including 127 during one survey — an unprecedented number. This year, a well-known right whale, dubbed Wart, appeared with a calf, prompting stunned researchers to conclude that she had given birth off New England instead of in the warm waters off Florida and Georgia where the whales normally calve.
“We don’t know what is going on,’’ said Mayo in the cabin of the Shearwater, as Christy Hudak and Beth Larson took plankton samples to study the relationship between food and right whale behavior and health.
Mayo said it is not yet clear if plankton is especially good in the bay and is luring more whales, or if it is declining somewhere else and driving the animals here.
Scientists say warming waters are probably causing some of the changes they are observing: Waters are warming off the Northeast — last year was the warmest ever recorded — and Mayo and others hypothesize the heat is causing changes in plankton species and their bloom times, ultimately altering whale behavior.
That is worrisome. If conditions change too dramatically and quickly, the whales may not be able to cope, researchers say.
And other threats are growing. Research shows the ocean is becoming noisier from ships and construction that may be interfering with the whales’ ability to communicate. New wind farms and oil and gas leases along the East Coast may soon contribute to that noise. Funding to study and understand the whales is threatened.
“The stressors are coming from multiple approaches,’’ says Rosalind Rolland, senior scientist with the New England Aquarium. “We are trending in the right direction, but one disease,or one oil spill” could cause a setback. “We are far from out of the woods.”Beth Daley can be reached at email@example.com. Follow her @Globebethdaley.