The bay scallops might look happy on first glance, fluttering about in the cold, briny tides of Menemsha Pond. But Chilmark shellfish constable Isaiah Scheffer knows water has the uncanny ability to distort reality. Just beneath the surface, he saw something was amiss.

“There have been a number of years recently where the scallops on the flats of Menemsha Pond have been much smaller than usual,” he said. “And we’ve been noticing a lot of weird stuff going on in Nashaquitsa Pond.”

Few spend as much time with the prized but notoriously fickle bivalves as Mr. Scheffer who, during his tenure as constable, has developed a keen eye for monitoring the health of his undersea charges.

That’s why at a recent shellfish conference a seemingly far-away problem caught his attention: the mass die-off of bay scallops in Long Island’s Peconic Bay, caused by a parasitic infection. Mr. Scheffer couldn’t help but wonder if the small Chilmark crop signaled that the Island’s scallops might be next.

The parasite hasn’t yet caused a wholesale collapse of the Island bay scallop population. — Ray Ewing

“It could be the canary in the coal mine,” he said. “They say we are about 20 years behind Long Island.”

As it turns out, his worries were no idle concern. The same parasite, of the family coccidia, that has decimated scallops in New York has recently been identified in multiple water samples from across the Vineyard and Nantucket. It is now assumed to be pervasive, and anecdotal evidence points to some illness in the Island stock.

Unlike in New York, the parasite hasn’t yet caused a wholesale collapse of the Island bay scallop population — a valuable data point for researchers looking to gain greater insight into the disease. But its arrival has scientists and aquaculture experts from New York and Martha’s Vineyard joining forces to look for answers.

Dr. Bassem Allam, a shellfish researcher at Stony Brook University, said that the first die-off in the Peconic Bay occurred three years ago, a major blow to a species that had spent the last four decades on the mend since the brown tide events of the 1980s.

“2019 was the first black year here in New York,” Dr. Allam said. “The population of adults has decreased 99 per cent, in some places 100 per cent. The fishery is really devastated.”

The situation in New York is a trend that Emma Green-Beach, director of the Martha’s Vineyard Shellfish Group, has followed closely from the start.

“They didn’t know what happened, they were like, ‘where did the scallops go?,” she said of the New York fishermen. “And every year since then they have had this same awful die-off.”

Although the parasite directly affects the scallops, it is not a danger to humans, officials said. According to the New York State Department of Environmental Conservation, the parasite “does not pose a public health threat but could significantly affect the bay scallop fishery.”

Dr. Allam seconded this. “The scallops are perfectly safe for human consumption,” he said. “These parasites are highly specific to their host.”

In 2020, the National Oceanic and Atmospheric Administration (NOAA) declared the New York situation a “fishery disaster,” unlocking federal and state research grants. Since then, progress has been made by Dr. Allam and his team, suggesting that part of the problem lies with warming waters but there are still more questions than answers.

The issue does not affect the much larger sea scallops which are found in deeper waters, officials said.

Bay scallops have a two-year life cycle. At the end of their first year they spawn, then spend the next year growing to a size big enough to harvest. The parasites strike after the scallops spawn, when the scallops are at their weakest, eating away at their kidneys and other organs until they die. This results in a species that lives long enough to spawn but then dies before growing large enough to harvest, leaving fishermen without their catch.

“It’s the worst-case scenario,” said Ms. Green-Beach. “But I think that is a reality we are all aware of.”

Finding solutions is also particularly challenging, she said, due to the timing of the parasite. With a typical shellfish disease, scientists would let infected scallops die and breed the survivors which presumably would have a genetic defense to the disease — a practice Ms. Green-Beach described as “old-school selective breeding.”

But in the case of the Coccidia parasite, the traditional strategy doesn’t work. Since death occurs after spawning, a scallop susceptible to infection is just as likely to pass on its genes as a healthy one.

“Selection might not actually be happening,” explained Mr. Allam.

To help save the bay scallop fishery, Ms. Green-Beach and Mr. Scheffer ­— who are married, making them an Island shellfish power couple ­— have begun working with Dr. Allam on a plan that they hope will unlock the shellfish’s genetic potential. The project involves a seed switch. Mr. Scheffer is now cultivating two strains of Long Island scallops in Menemsha pond, while Dr. Allam’s team is growing Vineyard varieties in Peconic Bay. Comparing the two will provide valuable data about how the different genetic groups respond to environmental changes. The seeds were scrupulously checked for disease before scientists made the transfer.

While the reason the Vineyard hasn’t been devastated is still uncertain, Dr. Allam believes water temperature may be a factor. Long Island waters have perhaps warmed to a dangerous threshold, Dr. Allam surmised, lowering baseline scallop health, and allowing the parasites to become more active. The trend does not bode well for the Vineyard stock.

“Long Island is warming, but so are we,” Ms. Green-Beach said.

Dr. Allam and his lab are exploring multiple possible solutions that range from incorporating genetics from different bay scallop subspecies to changing which season they seed.

Ms. Green-Beach also pointed to raising Island awareness of the problem as key, allowing researchers to find and test affected specimens, monitoring the disease in the same way that the Shellfish Group monitors dermo disease in oysters.

“They are already so rare, because they are so sensitive,” Mrs. Green-Beach said, outlining other difficulties the species faces, including acidification, salinity, water temperature and dwindling eelgrass. Still, she and Dr. Allam remain optimistic.

“Trust me, they are heartier than we believe,” said Dr. Allam, as he recalled all the extreme lab conditions his scallops had managed to survive. “There is hope. It’s not simple, but we have big hopes.”