The sun had not quite risen Thursday over Campobello as a small group of people clambered onto the 29-foot powerboat Nereid at a dock in the tidal narrows in Lubec. They quietly loaded camera cases, notebooks, electronic equipment, a cooler of food and other items onto the boat as they prepared for a daylong trip out into the Bay of Fundy.

Minutes later, after the crew of six had pushed off from the dock, two members zipped up their coats against the early morning chill and took their positions in the prow of the research vessel to look for marine life as they motored into Canadian waters toward Grand Manan Island. It was too early to know that, over the next 13 hours, they would see an estimated total of 42 right whales lounging and swimming in the bay between New Brunswick and Nova Scotia.

By 9 a.m., they were surrounded by more than a dozen of the creatures.

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Cunha didn’t mean someone had fired a weapon at the young male right whale that was lazily swimming only a few yards away. Cunha, who had a camera with a telephoto lens draped about his neck, was letting his boat mates know that he had successfully

taken a photograph of the whale that could be used to keep track of his travels and health.

This is the 30th year the aquarium has sent researchers to Lubec to conduct surveys of right whales. The photographs help researchers identify the whales by their scars and callosities, which are naturally occurring rough, white patches of skin on their heads. The photographs are incorporated into the North Atlantic Right Whale Catalog, a database maintained by the aquarium that researchers employ to keep track of where the whales have been, whether they are sick or injured and, if possible, when they were born and who their mothers are.

Such individual profiles are important because, when there are only 450 animals in a certain species left, each animal represents a significant percentage of that species’ gene pool.

This past winter, scientists recorded the births of 39 North American right whale calves off the coasts of Georgia and Florida, which is the highest number ever recorded during a single birthing season. But two of those calves already have died, they said, and with three-fourths of all right whales bearing scars from entanglements with rope or fishing gear, such a record year is not a guarantee of the endangered species’ long-term survival.

“That’s why this work is so valuable,” aquarium research scientist Amy Knowlton said on the Nereid. “The shipboard work is where you get a good look at the scars and see how deep they are.”

Ship strikes also are considered a significant factor in right whale injuries and deaths, but the aquarium’s annual right whale surveys in the bay have helped address this problem.

In the fall of 2003, because of the seasonal concentration of right whales east of Grand Manan, the main shipping lane that funnels large ship traffic in and out of the Bay of Fundy was shifted east toward Nova Scotia, away from where the whales tend to be found. In addition, whale researchers provide the bay’s shipping traffic controllers with information about the location of whales in the area, which then is passed on to the ships so they can know where the animals might be.

Moira “Moe” Brown, an aquarium research scientist who did not go out on Thursday’s trip, said the amount of ships that transit through the bay is not as high as it is elsewhere, such as in the waters off Boston or Jacksonville, Fla., but it is significant.

Approximately 1,000 ships come and go from the bay annually, she said.

Researchers occasionally put the surveys on hold in order to perform necropsies on whales that are found dead in the area, according to Brown. In 2006, a female right whale less than a year old was found floating in the bay and then dissected on Campobello. Scientists determined from the necropsy that the whale died from a ship strike.

“It’s arduous,” Brown said Thursday. “Taking a right whale down to the bone is not a minor undertaking.”

New England Aquarium’s annual surveys off Grand Manan date to 1980, according to Scott Kraus, the aquarium’s vice president for research. A proposal from Pittston Co. to construct an oil refinery in nearby Eastport prompted environmental scientists to conduct an aerial survey of the area in 1979, Kraus said, which revealed the nearby seasonal concentration of the whales. The aquarium’s boat-based research in the bay began the next year.

The whales’ heavy presence in the area really had been undocumented before then, in part because fishermen don’t set gear in the deep basin where they congregate, Kraus said. And in the 18th and 19th centuries, when whaling was an active fishery in the North Atlantic, the bay’s strong tides, confusing currents and frequently foggy conditions made the pursuit of whales too tricky for the sailing vessels used at the time, he said.

On Thursday, finding and photographing right whales took up most of the time of the Nereid’s crew, but the researchers made attempts to collect other types of information, too. On a few occasions, Knowlton dropped an underwater microphone over the side in an attempt to record a gunshotlike sound that male right whales make, the reasons for which are unknown.

They also made an attempt to collect a tissue sample off a young male who bore a significant entanglement wound in his fluke, or tail. The attempt failed when a dart fired from a crossbow by researcher Yan Guilbault missed its mark and the whale swam away.

The young whale was not the only one spotted Thursday whose entanglement has caused concern for whale scientists. A 6-year-old male whale researchers have named Kingfisher, who attracted heavy media attention in 2004 when he was found entangled in fishing gear off the coast of Georgia, was one of a handful of whales engaged Thursday in a social active group, or SAG, in the bay.

A SAG is when several whales interact by rubbing up against each other, slapping their flippers on the water’s surface and weaving around one another as they swim, the researchers said. SAGs usually involve one female and several males, researchers said, but some have been spotted with as many as 40 or 50 whales.

Kingfisher still might not have full use of his right flipper, but his perseverance five years after his predicament alarmed scientists and the public is a good sign, the researchers said.

“He looks healthy,” Guilbault said.

Aquarium scientists also have been known to collect samples of whale feces in the bay, but the research benefits of analyzing it has not been as fruitful as scientists once hoped it would be. But it can be useful if they know which whale it came from, they said. For a few years the aquarium even employed a dog trained to sniff out whale feces for the boat’s crew, but funding for the program dried up in 2006.

Though the smell of whale feces was in the air once or twice around the boat Thursday, none was spotted or collected.

There were plenty of distractions in the bay, but the aquarium staffers stuck to their mission of documenting the presence of right whales. Besides porpoises and several types of sea birds, pods of finback whales could be seen blowing multiple vertical sprays of water droplets in the distance, while even farther away humpbacks were occasionally seen breaching out of the water and then sending large splashes skyward as their bodies fell back down.

Guilbault said the weather is not good enough for researchers to go out every day they are in Maine. They try to go out frequently, he said, but are careful to spread out their trips over their two-month visit to make sure they stay within their budget.

There are times when they go out several days in a row, he said. They enjoy the work, but it can be tiring to spend three consecutive 14-hour days out on the water looking for whales.

“The third day, I can tell you, is a hard one,” he said.

A news reporter in coastal Maine for more than 20 years, Bill Trotter writes about how the Atlantic Ocean and the state's iconic coastline help to shape the lives of coastal Maine residents and visitors....