Scientists believe that one of the key threats to Puget Sound’s endangered southern resident population of killer whales is that they’re not getting enough to eat. That’s been a difficult problem to fix, in part because our knowledge of what they eat is incomplete.

The southern residents are known to depend heavily on Chinook salmon. But past studies have focused mainly on the whales’ diet during the summer months, when they spend lots of time in the inland waters of the Salish Sea around the San Juan Islands. Little was known about what they eat during the rest of the year, especially when they leave the Salish Sea to forage in along the Pacific coastline from California to Alaska.

Now, a study that compiles 10 years’ worth of data, gleaned from fecal samples and tiny fish scales scooped from stormy seas and analyzed with the latest genetic techniques, is making the picture clearer. The data suggest that the whales’ diets vary from season to season, shifting from primarily Chinook salmon during the summer months to a mixture of Chinook and coho in early fall, then Chinook, coho, and chum in the late fall. From January to March the southern residents have a more diverse diet that also includes fish species outside the salmonid family, before returning to nearly 100% Chinook in April and May.

“It really confirms the importance of Chinook salmon in the diet of these whales, all year long,” says study team member Lynne Barre, a marine biologist with NOAA Fisheries in Seattle. “But it also opens the door that there are more diverse species in the diet of the whales off the coast and in the winter months.”

A southern resident killer whale hunts a Chinook salmon. NOAA

To build this picture, researchers followed groups of killer whales in small boats and watched for signs that they might be hunting or sharing prey with other members of their pod. The researchers would swoop in after the whales finished eating and collect fish scales or bits of tissue left in the water, as if sweeping crumbs from the table after the whales’ buffet. They also collected scat – often visible like an oil slick on the surface of the water because of the whales’ penchant for fatty fish.

All of that, though, is easier said than done. “The weather during the winter is pretty lousy,” says Brad Hanson, a NOAA ecologist who led the sampling effort. What’s more, the outer coast waters are vast, and the whales tend to spread out much more than they do when foraging in the Salish Sea. “You can lose the whales two or three swells ahead of you.”

Despite such challenges, the team collected 81 fecal samples and remains from 152 predation events between October and May from 2004 to 2017. Back in the lab, they analyzed DNA in feces and scales to determine what species – and in some cases, which populations or stocks – the whales were eating.

They also identified individual whales based on body markings or DNA in the fecal samples. This enabled them to sort out the different dietary nuances of the three pods – J, K, and L – that make up the southern resident population. They reported their findings in a paper published March 3 in PLoS ONE.

The whales eat Chinook salmon from a wide variety of stocks, many of which are themselves endangered. In inland waters the whales eat Chinook mostly from Puget Sound and Fraser River runs. On the outer coast, about half of the Chinook they consume are from the Columbia River system, and most of the rest are from California Central Valley, Puget Sound, and Fraser River stocks. They eat non-salmonids such as lingcod, halibut, and big skate mainly in winter and in outer coast waters.

“This is really helping inform us where and when there might be gaps in the prey available to the whales,” Barre says.

The southern residents likely turn to a more diverse diet in the winter because their preferred Chinook salmon prey are less available, the researchers say. On the one hand, it’s good news that the whales are able to find alternative sources of food during the lean times of year. On the other hand, those alternative prey species might not measure up to Chinook.

“Chinook salmon are really tough to beat when it comes to energetic bang for the buck,” Hanson says. “They're a large fish to begin with, and then they have a very high fat content. So, in many ways they are the ideal meal for these whales, particularly for prey sharing.”

Boosting Chinook salmon stocks that the southern residents depend on in winter could be key to ensuring the whales’ survival. The data will help NOAA and other authorities prioritize salmon habitat restoration projects, fisheries regulations, and releases of hatchery fish.