A menhaden caught near Fire Island, N.Y., then inked and pressed directly onto rice paper using the traditional Japanese gyotaku printing method. CreditSteve Thurston

Branford, Conn. — In a bay near this coastal town, the sea was boiling with hundreds of herring-size shiners leaping to flee a marauding squad of bluefish. “These waters are coming back,” Bren Smith yelled above the shrieking din, as sea gulls plunged near our boat, scooping up fish. Mr. Smith grows seaweed and shellfish in Long Island Sound, and he says he’s seen a lot more action out here recently.

What thrilled me about this scene was that I was witnessing what happens when fishery managers set strict catch limits to stop overfishing.

Those leaping silvery fish were menhaden, also known as bunker, or pogies. To Mr. Smith and other fishermen I spoke to, there are encouraging signs that the menhaden population along the Atlantic Coast is healthy after decades of intensive commercial exploitation. Other sea creatures whose lives are intertwined with them also seem to be doing well. Sharks, whales, bluefish, tuna, osprey and other predators depend in part on these fish.

“There’s all this life that wasn’t there before,” John McMurray, who captains his own charter boat, told me. He said it’s been a boon for his sports fishing business off Long Island: “In the past four years, striped bass fishing has gotten a lot better, bluefish as well. We’re even getting bluefin tuna coming inshore to feed on the schools of menhaden.”

Menhaden are filter feeders. They swim in vast schools of hundreds of thousands of fish. Mouths agape as they feed, menhaden are living vacuum cleaners sucking up algae blooms that deplete inshore waters of oxygen and create biological deserts in the sea. A single adult menhaden can clean four to seven gallons of water in a minute.

The name menhaden is a corruption of “munnawhatteaug,” which means fertilizer in Algonquian. Native Americans taught the pilgrims to plant them with their corn, enabling colonists to coax a crop from rocky New England soils, according to Bruce Franklin, author of “The Most Important Fish in the Sea.” Bony and smelly, menhaden have rarely been caught for food. But their oil greased the wheels of America’s machine age after the Civil War, replacing whale oil as a cheaper alternative.

Today, menhaden oil continues to be sought, not as an industrial lubricant, but as a health supplement. Most of the 188,000-metric ton annual catch is rendered into heart-healthy omega-3 fatty acid fish oil. Much of the rest is used to produce fertilizers and high-protein feeds for chickens and pigs. In terms of weight, more menhaden are caught than any other fish on the East Coast.

But concerns that menhaden were being overfished led the Atlantic States Marine Fisheries Commission in 2012 to impose a quota that reduced the historic harvest by 20 percent. That limit was raised by 10 percent last year after regulators concluded that menhaden were not being over-harvested.

Now the fisheries commission is considering a proposal to expand the allowable catch by another 20 percent when it meets Wednesday in Bar Harbor, Me. The largest industrial menhaden harvester on the East Coast, Omega Protein, has suggested that the quota could easily be raised by up to 30 percent. The company points to the commission’s conclusion last year that menhaden were not being overfished. Critics of the 2012 quota decision say, moreover, that it was based on faulty methodology that identified a problem that didn’t exist; others argue that it understated the plight of the menhaden.

Regardless, the commission should keep the quota where it is and wait until a more comprehensive management approach is developed to safeguard this critically important fish.

That work is underway now. Scientists are developing reference points to measure the ecological role that menhaden serve as forage fish and how changes in their numbers would affect the predators that feed on them.

This would be a departure from the way most fish, including menhaden, are managed now. Regulators focus narrowly on how many fish of a particular species can be sustainably harvested. A decision on whether to adopt this more comprehensive approach is expected to be made next year.

Robert Ballou, the chairman of the commission’s Menhaden Management Board, said this method would enable “a new way of managing the fish that will credit them for their unique role in the environment and set quotas that are right, not just for menhaden, but for all of the species that depend on them.”

This is the right approach.

Setting quotas can be a messy process. Sports fishermen, commercial interests, state lawmakers and environmental groups often squabble over fishing quotas, and the limits that result can be split-the-difference compromises that leave nobody happy. And they can be environmentally catastrophic, when commercial considerations trump sound science. That’s what happened to New England’s groundfish fishery, including cod, which was declared a federal disaster in 2012.

This is why regulatory decisions need to be based not just on short-term profits but on the health of the ecosystem as a whole. This approach would be an enlightened departure for fisheries regulators, who typically see their job only as ensuring that specific fish stocks remain commercially viable.

Joseph Gordon, manager of mid-Atlantic Ocean Conservation for the Pew Charitable Trusts, said the commission’s effort to develop a holistic strategy for managing menhaden “is an incredibly exciting precedent. We are finally saying that we value this fish not just for what it provides when it is taken out of the ocean, but for what it provides when it is kept in the ocean.”

Until that approach is implemented, the commission should keep the menhaden quota where it is.

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