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“By-catch and discards,” Charles Clover wrote in The End of the Line, “are a fact of life to a fisherman.” More than 300,000 whales, dolphins, and porpoises perish in fishing gear each year, along with countless turtles, seals, sea lions, seabirds, and other marine creatures. To cut down on collateral damage, some fisheries employ excluder devices, special nets that allow unwanted animals to escape without forfeiting target fish. Australian fishers use seal excluder devices, or SEDs, while turtle excluder devices (TEDs) allow reptiles to pass through American trawls.

Excluder devices can prevent sea creatures from drowning in nets. They’re generally simple contraptions: angled, metal grates placed near the throat of the trawl allow fish to slip into the net’s back end, while deflecting larger mammals and turtles toward an escape hatch. But what becomes of animals after their encounters with trawls? Do they continue, unfazed, on their merry marine way? Or does the ordeal inflict lingering harm—even potentially causing death?

That’s the debate raging around the New Zealand sea lion, an endangered species that breeds primarily in the Auckland Islands, the rugged archipelago between New Zealand’s South Island and Antarctica. Since 1998, sea lion populations have plummeted nearly by half, to under 12,000 individuals. Many environmentalists blame squid fishermen, who harvested US $48-million in cephalopodic bounty from the Auckland Islands in 2016.

In the past, the squid fishery was an obvious culprit: in 1997 alone, fisheries observers witnessed more than 140 dead sea lions being hauled aboard the fleet’s decks. Since the early 2000s, however, squid trawlers have deployed sea lion excluder devices (SLEDs). By 2011, observed sea lion casualties had fallen to fewer than 10. Problem solved, right?

Not according to Stefan Meyer, an ecologist who recently completed his PhD at New Zealand’s University of Otago. Meyer thinks that the squid fishery is still responsible for sea lions’ ongoing decline, even if the deaths are less obvious.

Analyzing by-catch and sea lion population data, Meyer and his colleagues found that the estimated rate of sea lions passing through excluder devices correlates closely with pup production—that is, the more sea lions enter nets, the fewer pups are born. To Meyer, that proves that fishing remains the most important factor constraining sea lions, suggesting that nets are hurting them in spite of SLEDs.

“If you turned off fishing, the population would grow,” Meyer says.

According to Meyer, SLEDs haven’t saved sea lions—they’ve merely masked the casualties. Observers are no longer seeing scores of drowned sea lions, but that doesn’t mean the trawls aren’t harming the animals, he says. Perhaps sea lions suffer concussions or internal injuries during their collisions with the metal grates. Perhaps their drowned bodies fall from nets before they’re hauled aboard. Or perhaps being ensnared, even temporarily, so stresses females that they abort their pups.

But this “obscured mortality” hypothesis has detractors—and not just fishing industry representatives, who called the paper “vague and contradictory.”

Excluder devices offer a way for non-target species to escape, while keeping fish trapped. Video by the Australian Fisheries Management Authority

In a letter to the New Zealand Herald, a trio of prominent sea lion researchers criticized the study’s methods. Fishing pressure in the Auckland Islands can vary by an order of magnitude from year to year, depending on environmental conditions and market forces. In 1996, for instance, 4,500 trawls swept the Auckland Islands, but in 1999, the number plunged to 400. The dissenters claim that by basing their calculations on the interaction rate—the number of sea lions encountering each squid trawl—rather than the total number of interactions between sea lions and nets, Meyer’s group failed to account for those fluctuations in their model. “When you relate total interactions to changes in pup counts,” the detractors write, “there is no relationship.”

Among the objectors was Jim Roberts, an ecosystems modeler with the New Zealand National Institute of Water and Atmospheric Research whose work informed the government’s sea lion management plan. Roberts’s own assessment, published in 2016, found that the sea lion population would continue to decline even if trawls didn’t kill a single animal, suggesting that other threats are likely causing the continued collapse. That squares with previous studies that showed that sea lions probably don’t crash into SLEDs hard enough to incur fatal concussions, and that necropsied sea lions that had apparently been hurt by SLEDs had actually sustained the damage after death, when their bodies were frozen for preservation.

But if by-catch isn’t the smoking gun in sea lions’ plight, what is? The short answer is that no one quite knows.

Roberts points the finger at a bacterial infection called Klebsiella, as well as pups’ unfortunate tendency to be killed by large males or drown in mud holes. Great white shark predation could be a factor, too. And just because sea lions aren’t dying in nets doesn’t absolve fisheries. It’s possible the industry, along with changing ocean conditions, is depleting the squid, hake, and cod upon which sea lions depend.

“Advocates prefer a simplistic message, but in ecology the problems tend to be quite complex,” Roberts says.

Whatever’s causing the New Zealand sea lion decline, the larger question that Meyer’s study raises—what happens to animals after they meet excluder devices?—remains an important, and little-examined, one.

Jeff Gearhart, a Mississippi-based biologist with the US National Oceanic and Atmospheric Administration, studies TEDs by diving to the seafloor and deliberately passing captive two-year-old loggerhead turtles through trawls. His and others’ research has shown that 97 percent of turtles safely navigate TEDs, and Gearhart credits the devices for the rebound of Kemp’s ridley sea turtles. “Is there latent mortality happening? It’s possible, but we don’t think so,” he says. Still, whether turtles that endure TEDs ultimately fare as well as ones that don’t remains a mystery.

In the case of sea lions, Meyer says that uncertainty justifies a precautionary approach. Bruce Robertson, a University of Otago zoologist who worked alongside Meyer, proposes that squid vessels switch from trawls to jigs, a hook-based system that would avert by-catch. (Industry representatives claim that switching gear would be prohibitively expensive.)

“Excluder devices for all marine megafauna have good intentions,” Meyer says. “But it’s important to monitor population trends and reproduction to make sure they’re actually working.”