How much of orca decline is in their DNA? - Salish Current
December 9, 2022
How much of orca decline is in their DNA?
Kai Uyehara

A Southern Resident killer whale calf breaches alongside a pod-mate in the Puget Sound. These icons of the Northwest are endangered, their population is in decline and their chances of recovery are unsure. (Courtesy Brad Hanson, NOAA Northwest Fisheries Science Center)

December 9, 2022
How much of orca decline is in their DNA?
Kai Uyehara


The Southern Resident killer whales (SRKW) in J, K and L pods — black and white icons of the Northwest — migrate between Northern California and Alaska, but reside in Puget Sound and the Salish Sea from late spring through fall. Icons that they are, nonetheless these top predators are endangered. Their population is in decline and their chances of recovery are unsure. 

This year’s count of 73 whales is two more than the number of whales first recorded after the pods were decimated by captures from the ’60s to mid-’70s. Recovery reached a high point of 97 whales 26 years ago, then steadily declined. Biologists and advocates alike wonder whether the Southern Residents can recover and survive with such a small gene pool … or are they doomed to extinction.

Only a few females are producing, said Brad Hanson, wildlife biologist at the National Oceanic and Atmospheric Administration (NOAA) Northwest Fisheries Science Center, and they’re producing viable calves sporadically. 

Recovery has focused on understanding the effects of declines in prey quantity and quality, vessel traffic, exposure to toxic contaminants and inbreeding within the small population, and what can be done. Advance technologies allow scientists to sequence entire Southern Resident genomes, providing another tool in research and recovery. 

Only 20 to 25 of the 73 Southern Residents are breeding, said Mike Ford, director of the Northwest Fisheries Science Center’s conservation biology division. “Over time, you can’t really avoid inbreeding in a population that small,” Ford said. 

Four individuals are the offspring of a father-daughter and mother-son pair, but all four are still alive, and there may be others that are inbred to a lesser degree.  Ford says he doesn’t think they’re inbreeding on purpos, but rather not paying attention as there are many relatives in the small population. 

Southern Resident killer whales stay with their mothers and families throughout their lives instead of leaving to join new family groups.

Looking for answers in DNA

While this strategy may be somewhat beneficial, the resulting inbreeding has its consequences. The lack of genetic diversity in an animal’s genome resulting from two relatives rearing offspring leads to a much higher chance of poor health, lower reproduction and survival, Ford said, and threatens their chances for recovery. 

Data on vital signs on the Puget Sound Partnership website includes a count of the number of Southern Resident killer whales each year since 1973. This year’s count is just two higher than when captures were ended.

Scientists previously studied SRKW lineage by using only a small portion of the animal’s genome to establish paternity. Now Ford and NOAA are collaborating with The Nature Conservancy and BGI, a global genomics company, to sequence the entire genome of many SRKW to determine if issues related to inbreeding will prevent the whales from recovering.

The sequencing, too expensive only 20 years ago, will now help scientists quantify how inbreeding limits population growth, Ford said. 

A fully sequenced SRKW genome might also give scientists a look at the genetic variations and immune system genes that are important for the whales’ survival, and offer a better understanding of the population’s history and size prior to European colonization, Ford added. The information could also verify current pedigrees and aid scientists in comparing Southern Residents with Northern Residents and other similar populations that are thriving, to determine what factors are setting them apart.

“If you want to have the highest success of recovering the Southern Resident killer whale population, you have to have as good information as possible on what is limiting its recovery,” Ford said. “Otherwise you might be spinning the wheels, working on things that may or may not be important.”

Getting a more detailed understanding of the Southern Residents’ inbreeding problem will also bring the limiting-factor conundrum full circle. 

“The more accurate a measure you have of exactly how inbred a particular individual is, you can basically filter out some of that noise and detect the signal that you’re interested in,” Ford said. “Inbreeding, even if it’s important, is not going to be the only thing impacting the survival or reproduction of these whales.”

The Southern Residents have fascinated Hanson since childhood. Every time he sees one breach after its unseen activities underwater, he’s as thrilled as ever. As to whether they can recover and survive, Ford takes a neutral approach.

Hanson takes a glass half-full approach by considering the mystery that shrouds their origins, the Southern Residents’ “founding event,” where they may have grown from a very small initial population. If they did it once, perhaps they can do it again. 

But for now, Hanson said, the population is small and there aren’t many juvenile females to reproduce; the SRKW population will continue to decrease for the foreseeable future. Killer whales have long lifetimes, so many people alive right now may not see that rebound if it happens, he said. In the wild, females can live up to 90 years old, and males to 60.

The problem with prey

Today’s SRKW are not living now as at the time of their “founding event,” but are beset by the threats of diminished prey, chemical pollution, loss of spawning and rearing habitat and underwater noise.

The relationship between a decline in Chinook salmon prey and Southern Resident populations is evident, but there is no simple explanation for the decline of the orcas, Hanson said. 

The Southern Residents prey almost exclusively on Chinook returning to the Fraser, Skagit, Snohomish and other rivers entering the Puget Sound, according to NOAA. 

Chinook are the best bang for their buck, Hanson said; they are the largest of the salmon, have a high fat content and yield the most energy-dense catch for an orca. 

But Chinook salmon are returning from the ocean to their natal streams in fewer numbers, are smaller in size and return at younger ages. In all, there are fewer and smaller fish to eat.

Orcas need 300 to 450 pounds of food per day, said Deborah Giles, science and research director for Wild Orca, an advocacy and research group. Now that the average size of a Chinook is twelve-and-a-half pounds, orcas need to forage longer to meet their caloric needs. 

Southern Residents could rely on halibut, skate, lingcod, steelhead and coho salmon, but not all prey provide the same energy and caloric content as Chinook, Hanson said, and they may require more energy and time to catch. Scientists at NOAA are still seeking a better understanding of the orcas’ prey requirements. 

Beyond that, Giles says the Southern Residents are not being treated as stakeholders when NOAA and fishery managers divide up the salmon population left after Alaskan fisheries collect and the treaty-protected portion of salmon is allotted to the Coast Salish tribes. 

Wild Orca is advocating for the consideration of the Southern Residents’ prey needs in fishery management discussions and changes in Alaskan fishing to avoid the decimation of Pacific salmon populations that have traveled up into Alaska — never having originated there — before they can migrate back down south. 

Activists like Giles are fighting for the Southern Residents’ right to their natural food supply.

In August, a federal judge in Seattle found that the National Marine Fisheries Service endangered the SRKW by failing to allocate for them sufficient Chinook salmon during the Southern Alaska salmon harvests.

Meanwhile, the issue of orca legal rights moved forward on Monday when the city’s mayor signed a proclamation urging local, state, federal and tribal governments to protect the orcas rights to life, autonomy, culture, free and safe passage, adequate food supply and protection from harm. 

The Southern Residents face a slew of legacy chemical contaminants that don’t break down over time, such as the banned Dichlorodiphenyltrichloroethane (DDT) and Polychlorinated biphenyls PCB) as well as Polybrominated diphenyl ethers (PBDEs), a compound used in clothing as a flame retardant.

Chemicals from municipal and industrial discharges and street runoff enter the Salish Sea food chain and bioaccumulate in Chinook salmon preyed upon by SRKW. 

“The whales get contaminated by way of consuming prey,” Hanson said, and that may predispose them to many diseases that could hinder their metabolism or diminish their appetite, giving the false appearance that the orca is starving from a lack of prey. 

Because of their longevity, orcas continue to accumulate toxic chemicals. Male orcas retain the chemicals in their fat, while a female will transfer 85% of her chemical contamination to her offspring during lactation. 

Southern Residents can be seen in the Puget Sound right now in the Salish Sea, as were these seen breaching offshore near Seattle at the beginning of the month. (Courtesy Brad Hanson, NOAA Northwest Fisheries Science Center)

Hanson said that transient killer whales, which are carnivorous, are also highly contaminated and have a thriving population. However, unlike SRKW who only prey on limited numbers of Chinook, the prey of transients is not limited.

Navigating through vessels

“The Strait of Juan de Fuca is a pretty noisy place because of not only what’s there, but also the configuration of it,” Hanson said. Noise from commercial vessels bounces off steep rock walls around the San Juan Islands where the orcas forage.

Large ships emit mostly low frequencies but may have higher frequencies mixing with the higher frequency emitted by smaller recreational and fishing boats, Hanson said. Orcas use high-frequency echolocation to navigate and forage.

“What we’re really concerned about is when you have all of this additional noise that is potentially in these important frequency bands for the whales, that it just reduces the detection distance for the whales,” Hanson said. That may make foraging more difficult. 

Scientists at NOAA have discovered that the Southern Residents were essentially raising their voices to overcome their noisy environment, a phenomenon called the Lombard Effect,.  

Orcas forage less with vessels within 400 yards, diving less and spending less time in a deep foraging state to capture salmonid prey, NOAA found. This effect was especially prominent in females, underscoring how vessel traffic disrupts prey sharing when females are feeding calves. 

Currently, Washington regulations require that vessels stay at least 300 yards from the orcas laterally, and no less than 400 yards in front of or behind them, a rule put in place by the Washington Department of Fish and Wildlife which also requires boaters to reduce speeds and temporarily turn off depth finders when Southern Residents are nearby.

A new report from the Washington Department of Fish and Wildlife this month has recommended the buffer be extended to 1,000 yards to further support orca recovery, based on information and science gathered since the original rules were adopted two years ago.

Notwithstanding whether genetics will determine the fate of the Southern Residents, government entities, organizations and individuals will continue working on many fronts for the recovery of these iconic marine creatures.

“There’s been a lot of people working on this,” Hanson said. “We have lots of great collaborators and colleagues that have been working really hard.”

“We seek out meetings with elected officials so that they can be made aware of the most recent science and then we push for policy to be changed so that the whales have a place at the table,” Giles of Wild Orca said.

“Everything we do has an environmental impact — just start with being environmentally conscious,” Hanson said. “It’s an enormous area that these whales are dependent on for fish.” 

— Reported by Kai Uyehara

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