A new scientific study says extremely rapidly warming waters off the New England coast have had a severe consequence — the collapse of a cod fishery that saw too many catches, even as overall cod numbers declined because of warmer seas.

It’s just the latest in a series of findings and occurrences — ranging from gigantic snows in Boston earlier last winter, which scientists partly linked with warm seas, to a sudden and “extreme” sea level rise event in 2009-2010 — suggesting that this particular stretch of water is undergoing profound changes.

“[In] 2004 to 2013, we ended up warming faster than really any other marine ecosystem has ever experienced over a 10 year period,” said Andrew Pershing of the Gulf of Maine Research Institute, lead author of the new study just out in the journal Science. Pershing conducted the work with researchers from his institution and several others in the U.S. including NOAA’s Earth System Research Laboratory in Boulder, Colorado, and Stony Brook University in New York.

The paper reports that during the decade-long period in question, the Gulf of Maine, the ocean region extending from Cape Cod northeast to the southern tip of Nova Scotia, warmed up by a truly stunning 0.41 degrees Fahrenheit per year. That’s faster warming than occurred in 99.9 percent of the rest of the world ocean, the scientists say.

During the same time, this fishery’s managers did reduce quotas but not enough — presumably because of a lack of realization about the rapidly warming waters and their stark effects on fish. As a consequence, the overall cod stock now stands at just 4 percent its optimum size.

Last November, the National Oceanic and Atmospheric Administration announced sharp restrictions on cod fishing in the area, with harsh consequences for fishing dependent communities such as Gloucester, Massachusetts.

“The Gulf of Maine cod stock, a historic icon of the New England fishery, is in the worst shape we have seen in the 40 years that we have been monitoring it,” John Bullard, NOAA Fisheries regional administrator for the greater Atlantic region, said at the time.

At the center of the new study is a demonstration of just how tightly this is related to warm waters.

The effect of warm waters on Atlantic cod likely occurs because of a harmful effect on larvae and juvenile fish, but the scientists say they don’t fully understand whether it is related to changes in cod predators or prey or simply the temperature itself. Warmer temperatures also pose a metabolic challenge to cod as they reach critical reproductive age.

The disaster for the fishery wasn’t caused by temperatures alone, however — it also was caused by how humans failed to take them into account, the researchers charge.

“Ignoring the influence of temperature produces recruitment estimates that are on average 100 percent and up to 360 percent higher than if temperature is included,” the researchers said. Thus, in effect, they say cod were overfished because ocean warming wasn’t adequately considered in fishing quotas.

The effect has not, to be sure, been the same for all species. Take lobsters, for instance, which are thriving in the same waters.

“They’re the flipside of cod,” Pershing said. “They are booming now, especially off the coast of Maine, and that’s due in part to the fact that there are fewer cod which eat lobsters but also due to the warmer water, which helps them grow faster.”

The consequence of the dramatic downturn for the cod fishery has likely been significant for some fishing communities, though there are no definitive data on the matter, said Pershing’s colleague Jen Levin, who manages the sustainable seafood program at the Gulf of Maine Research Institute. But Levin said the availability of cod on people’s plates hasn’t changed much, because globally other fisheries are doing far better, such as in the Bering Sea.

“From an industry perspective, seafood is one of the most traded commodities on the planet, so as far as what’s available on the marketplace, you can still find cod, it’s just not from here, it’s from other parts of the world,” Levin said.

What’s most intriguing is what is causing the dramatically warm waters — and how this may relate to other observed changes in the region.

Clearly, part of the cause is the overall ocean warming trend that has been seen around the globe due to climate change. But at the same time, the researchers say, the warm and salty Gulf Stream has moved northward more throughout the last century — a change that also has been linked to a warming climate but for more complex reasons. In late 2011, in fact, there was a dramatic northward movement that led to the warming of some New England lobster traps by more than 6 degrees Celsius, or over 10 degrees Fahrenheit.

Among other factors, the northward shift of the Gulf Stream appears tied to a larger change in Atlantic ocean circulation — the slowing of the Atlantic Meridional Overturning Circulation, or AMOC, which carries warm surface water northward and cold water southward at depth and is driven by differences in temperature and salinity of these waters.

“AMOC interacts with the bottom of the ocean and when it slows, the interaction with the bottom causes the Gulf stream to shift north,” Michael Alexander, one of the study authors and a researcher at NOAA’s Earth System Research Laboratory in Boulder, Colorado, said by email. “Once the Gulf Stream shifts north some of the warm water it carries is able to work its way into coastal waters, including the Gulf of Maine.”

“There are long-term changes in ocean circulation in the North Atlantic, most likely driven by anthropogenic climate change, that have led to a ‘ cold blo[b]’ in the subpolar central North Atlantic, but might actually be responsible at least in part for the anomalous warmth in the far western North Atlantic,” added Penn State University climate researcher Michael Mann, who reviewed the study for The Washington Post. In effect, the idea is that as less warm water moves north into the waters below Greenland, there’s more that can linger off the U.S. East Coast.

The consequences of these changes may be affecting far more than cod and the people who fish for them.

For instance, a slowing of the AMOC also was recently associated by scientists with a sudden and dramatic 4 inch East Coast sea level rise event in 2009 and 2010. Slowing the circulation is expected to cause U.S. sea level rise because it weakens the contrast between warm waters to the right (or European side) of the Gulf Stream and cooler waters on its left (or American side). Warm water is less dense than cold water. It thus takes up more space.

Scientists such as Mann also have linked warm ocean temperatures off New England to the dramatic snowfalls that Boston experienced earlier this year — noting that warmer water means there is more moisture in the atmosphere above it. And this moisture, if swept up in a storm, can produce more precipitation.

In sum, it’s all part of a bigger picture, Mann said.

“That warmth is implicated, in this latest study, for the dramatic decrease in Gulf of Maine cod populations, and it is likely also responsible for the northward retreat of cold water-loving sea life including the iconic Maine Lobsters. These unusually warm seas also contributed to the nor’easters last winter that generated record snowfalls in New England. Those storms feed off warm seas both for their intensification, and for the amount of moisture that is available to produce snowfalls.”

And research to understand the other consequences of such stark ocean warming in the Gulf of Maine and off of the coast of New England has only begun.

“We’re seeing an ecosystem going through a really massive change, and I really want my colleagues to look at this. We need to understand what it means,” Pershing said.