The killer whales that summer in Puget Sound have been breeding within their own family groups, raising concerns among scientists that the region's troubled orca population actually may be more fragile than once thought.

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The killer whales that summer in Puget Sound have been breeding within their own family groups, raising concerns among scientists that the region’s troubled orca population actually may be more fragile than once thought.

While the endangered southern resident orcas in J, K and L pods avoid mating with siblings or offspring, a significant number of young whales in recent years have been born to parents that are members of the same pod, according to a new study by several of the Northwest’s top orca scientists.

That trend surprises and worries researchers who say it could significantly reduce the population’s genetic diversity, making whales more susceptible to disease and genetic disorders or mutations. Such “genetic bottlenecks” can also reduce the ability to withstand environmental upheaval, such as toxic pollution or climate change.

“It shows that the population is fairly inbred,” said University of Washington professor Sam Wasser, one of the study’s authors. “And that may have a lot of repercussions for recovery. Inbreeding tends to exacerbate all their other problems.”

Lead author Michael Ford said the picture isn’t completely dire. Some of the whales also breed outside their pods, and “a little bit of outside breeding can go a long ways.”

It’s also not clear whether the southern residents have always bred this way or have somehow been forced to change mating patterns over time as the population declined.

“In terms of how bad it is … that depends on how long the population size stays small,” said Ford, a scientist with the National Marine Fisheries Service’s Northwest Fisheries Science Center in Seattle. “Brief bottlenecks don’t necessarily have to have a long-term impact. But as a general rule, we should be concerned about small population sizes because genetic diversity is the raw material for adaptation and evolution.”

Southern residents currently number between 85 and 87, down from a high of 97 about 15 years ago. Researchers have long believed the southern resident orca populations historically reached 120 to 200, though Ford’s study suggests it actually may have been higher. The whales were listed for protection under the Endangered Species Act in 2005.

The study, published this month in the Journal of Heredity, was an attempt to unravel a few basic riddles.

Through decades of observation, by the Center for Whale Research in Friday Harbor and others, biologists understand a lot about orca maternity.

“We know who everybody’s mom is for every animal since the 1970s,” Ford said. “But we know nothing about their fathers.”

While researchers see a fair amount of whale interplay that could be sexual activity, actual paternity has been a mystery because mating takes place out of sight.

So for four years, researchers gathered DNA samples from the mucous of live whales and from floating feces spotted by scat-tracking Labradors led by Wasser. They also took blubber and skin samples from stranded and long-dead whales. All told, they examined the DNA from 78 mothers and calves and potential dads. And they used the genetic information to begin building family trees.

The researchers had presumed the whales never mated within their own pod, because studies have shown that to be true of northern resident whales in Canada. But they were wrong.

They found that mating was dominated by a handful of aging males, the oldest of which, J1 — dubbed Ruffles, for his wrinkled dorsal fin — fathered at least five calves just in J-pod. The other top breeding male, L41, also produced offspring from an L-pod female.

Ford isn’t entirely sure how to interpret the findings. Since most of the inbreeding involved a single male, it could be a factor of Ruffles’ idiosyncrasies. When a new generation of young males starts reproducing, the inbreeding pattern could change. (Ruffles is believed to have died sometime in the past year at nearly 60 years of age.)

It also may be related to the loss of so many breeding-age adults during the 1960s, when southern resident killer whales were rounded up in pens and sold to theme parks.

It’s concerning because inbreeding can compound existing problems.

“It means a lot of peripheral things could be impacting their health more than we thought,” Wasser said. “This sort of touches on everything.”

For example, southern residents feed almost exclusively on chinook, even when sockeye are abundant — probably because chinook are fattier and more nutritious, and “almost certainly because over their evolutionary history chinook was so plentiful,” Wasser said.

But a lack of genetic diversity may hurt efforts to change their eating habits as chinook numbers continue to decline.

Meanwhile, inbreeding can also result in a greater possibility that an offspring is male, Wasser said, and K and L pods in recent years have produced mostly male calves. That could alter reproduction in the future.

The study, researchers concluded, puts greater importance on figuring out exactly why the population is not rebounding faster.

“When you have a rapid decline, you expect a rebound, but they’re just not rebounding,” Wasser said.

Craig Welch: 206-464-2093 or