Inbreeding is contributing to endangered killer whales decline

Inbreeding is jeopardizing the recovery of an endangered population of killer whales, causing their numbers to fall at a time when many other killer whale populations are on the rise.

In a recent study published in Nature Ecology and Evolution, researchers found Southern Resident killer whales’ (Orcinus orca) low numbers weren’t just a result of their difficult recovery. They were one of the causes of their decline in the first place. Inbreeding in the small population caused many whales to die at a young age—before they had time to reproduce. Past research found that just two males were responsible for most of the reproduction, making inbreeding an even greater problem.

“The thousand-dollar question with Southern Residents is why this population was not doing well, not growing, when almost all of the other Northern Pacific populations were growing substantially,” said Marty Kardos, research geneticist at NOAA Fisheries’ Northwest Fisheries Science Center and a lead author of the study. “It looks like a big part of the reason the Southern Resident population is declining, despite being protected, is because they’re inbred.”

Southern Resident killer whales swim along the West Coast of North America, from California to southeastern Alaska. Their name stems from the fact that they occur farther south than their Arctic neighbors.

Like other killer whale populations, they have suffered toxic pollutants and disturbance from ships and other vessels. While their numbers have probably never been high, marine park captures and accidental deaths in the process reduced their population even further.

“We took this population that was already small and already on the edge of the distribution of resident killer whales in the North Pacific and Arctic and decreased their population size by capturing and killing all these individuals,” Kardos said.

After captures ended in 1976, their numbers climbed. In the 1990s they neared 100 individuals but now number just 73—about where they were before protections were put in place. In 2016, NOAA Fisheries identified them as one of eight marine species most at-risk of extinction.

The inbreeding problem isn’t a complete surprise. NOAA Fisheries’ 2008 recovery plan noted that the population’s small size “makes it potentially vulnerable” to inbreeding, but because Southern Residents have rebounded from low numbers before, “the factors responsible for the decline are unclear.” And other marine mammals, like northern elephant seals (Mirounga angustirostris), have bounced back from near extinction without obvious setbacks from inbreeding.

Combining modern genomics with decades of field observations, the new study offers the first major findings from the sequencing of the Southern Resident genome. Beginning in 2018, researchers on the project decoded the DNA of about 100 Southern Residents. They also looked at whales from other populations in the northeast Pacific.

The research showed that inbreeding is causing many of the whales to die before they can reproduce. Killer whales first reproduce at about 10 years old and reach their reproductive prime around 20 years old. Highly inbred Southern Residents had about half the chance of reaching 40 years old than less inbred whales. While less inbred females were producing an average of 2.6 calves—enough to at least sustain the population—the most inbred females were producing an average of 1.6 calves. The result is that inbreeding depression appears to have limited recovery and will likely cause the population to continue to decline in the future.

The whales’ behavior makes it harder to counteract the effects of inbreeding. Although Southern Residents are often in close proximity to other killer whales, they don’t mate with them. They even sing different songs. Translocating other whales is unlikely to be successful in helping the Southern Residents, Kardos said. And while captive breeding programs have helped some struggling wildlife populations, Southern Residents are unlikely to welcome newcomers.

If there is any good news in the findings, Kardos said, it’s that the level of inbreeding is fairly low and the projected decline is slow. Environmental protections have helped sustain the whales so far, he said, and they will be needed in the future to allow the population—which is beloved by Pacific Northwest whale watchers—to continue.

“The best shot at recovering this population is ensuring that they have as good an environment as we can give them and protect them from direct harm,” he said.