A new study nails dearth of chinook salmon as the primary cause of the endangered resident orca whale’s failure to rebound.

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A team of researchers has isolated lack of food as the primary factor — bigger than vessel traffic, bigger than toxins — limiting recovery of resident killer whales.

In a paper published Thursday in PLOS ONE, a team lead by Sam Wasser, professor of biology and director of the Center for Conservation Biology at the University of Washington tracked the nutritional, physiological and reproductive health of southern resident killer whales — the J, K, and L pods of orcas that frequent the Salish Sea, including the San Juans and the waters of Seattle.

The study links low reproductive success of the whales, with a total population of just 78 animals, to stress caused by low or variable abundance of their favorite prey: chinook salmon.

Scientists continue to evaluate the role of vessel traffic, including whale-watch boats, toxins, and food supply in the orca’s troubles. Wasser said his results point to food as key.

“It’s the fish,” said Wasser, whose team found that of 35 pregnancies among whales tracked from 2007 to 2014, only 11 produced a live calf.

The females with failed pregnancies had levels of hormones indicating nutritional stress seven times higher than females that successfully gave birth.

“Pregnancy failure — likely brought on by poor nutrition — is the major constraining force on population growth,” Wasser said of resident orcas, a federally listed endangered species since 2005.

The number of pregnancies lost was actually probably higher: The team was unable to detect the earliest months of pregnancy, which is when failed pregnancies typically occur.

Deborah Giles, research director at the nonprofit Center for Whale Research, and an author of the paper, said vessel traffic and toxics and lack of food are all bad for the whales, but when whales are well-nourished, other problems don’t affect them as much. “If the whales are well-fed, you don’t see a strong signature for stress hormones related to vessels,” Giles said. “They are going through problems of famine and deeper famine.”

Some aren’t convinced lack of food is the orca’s biggest threat. “It is complicated,” said Brad Hanson, wildlife biologist with National Oceanic and Atmospheric Administration (NOAA) Fisheries, who has used acoustic sensors and tags to track the whales’ movements, and study how vessel noise affects them.

Noise is actually a piece of the food problem, Hanson said. Prey has to, of course, be available for the whales, but they also must be able to find it. Orcas seek and find their prey by echolocation, which can be overwhelmed by the racket of container ships and whale-watch boats and other vessels.

Unanswered is why the orcas are so adamant about refusing other foods. That they would choose the largest, fattiest salmon — chinook — makes sense, in terms of targeting hunting effort at the most calories. But Hanson has watched orcas kill harbor porpoise and even tote them around under a fin, or push them along with their nose, yet never take a bite.

It’s just not part of the resident orcas’ culture to eat marine mammals, Hanson said. With distinct languages and family groups that pass on the knowledge of what to eat, where to catch it and how to share it, resident orcas likely aren’t changing their diet anytime soon.

Wasser said a lack of food also makes orcas burn their body fat, which in turn releases toxins bound up in the fat — from flame retardants to DDT — further suppressing their reproductive health. “It’s a double whammy,” Wasser said.

To do its research, the team deployed a trained dog in the bow of the boat capable of catching the scent of whale scat on the water from up to a nautical mile away. The team collected 348 scat samples from 79 orcas between 2007 and 2014.

The method is unique, allowing collection of samples in the wild and noninvasively that reveal intimate information, from pregnancy to stress levels and even types of stress the whales are under.

The team also compared hormone data to records of chinook salmon runs in the Columbia and Fraser River, and saw large runs at those watersheds coincided with periods of lower nutritional stress in the orcas, and vice versa.

“The take-home message is we really have to start looking at how to restore these fish,” Wasser said. That includes habitat fixes to boost salmon runs, including on the Columbia, where big, fatty spring chinook are a critical source of nutrition for the orcas in the early spring, carrying them until summer’s Fraser River runs, Wasser said.

“Should we take out the Lower Snake River Dams? I don’t know, but we have to start looking at that,” Wasser said. “People are shying away from that, but it has to be investigated as a fix.”

A federal judge has sent NOAA Fisheries back to the drawing board to determine an operation regime for the federal Columbia River hydropower system that does not jeopardize threatened and endangered salmon runs in the Columbia and Snake, its main tributary. The judge ruled in a 2016 court decision dam removal must be on the table.