Over the past 7000 years, Chinook salmon in the Columbia River have lost two-thirds of their genetic diversity.

Rich Landers/The Spokesman-Review via AP

Pacific Northwest salmon are in big genetic trouble

Chinook salmon, an iconic species in the Pacific Northwest, have lost up to two-thirds of their genetic diversity over the past 7000 years, researchers report. The finding underscores a long-held concern that future salmon populations are imperiled by a combination of stream habitat loss, overfishing, dams, and the release of millions of fingerlings from hatcheries—even as the fish try to respond to climate change and ocean acidification.

“It’s a fascinating report,” says Matthew Sloat, a fisheries ecologist with the Wild Salmon Center, a nonprofit salmon conservation group in Portland, Oregon. “The main conclusion is not terribly surprising,” he says, but “it does confirm a long-standing guess that there has been a broad loss of genetic diversity in the [Columbia River] Basin.”

Genetic diversity is often key to enabling a species to adapt to changing environmental conditions. In salmon, for example, some individuals or populations might carry genes that make them less susceptible to new diseases or warming seas, enabling the species to survive the loss of other genetic strains.

In Chinook salmon, part of the diversity loss is undoubtedly the result of an overall decline in Chinook populations. From the late 1880s through the early 1920s as much as 11 million kilograms of Chinook were harvested each year. That number has dropped to about 2 million kilograms per year today. But roughly half of these fish originate in hatcheries that release fingerlings that are far more genetically similar than wild populations. Other factors have also contributed to the loss of diverse wild salmon populations, including destruction of stream habitats, water diversions for agriculture, and the construction of more than 400 dams across the Columbia River Basin and its main tributary, the Snake River. The dams prevent salmon from reaching more than half of the river system’s spawning habitat.

To quantify just how much genetic diversity Chinook have lost, researchers at Washington State University (WSU) in Pullman and the University of Oklahoma (OU) in Norman turned to ancient DNA. Working with several Native American tribes, they collected a trove of 346 samples of vertebrae from archaeological sites at Native American garbage piles, or middens, some dating back 7000 years. They then analyzed each sample’s mitochondrial DNA, which is typically more abundant—and thus easier to recover—from archaeological samples than nuclear DNA. Initially they looked for genetic markers that indicated the vertebrae came from Chinook salmon, says Bobbi Johnson of WSU, who carried out the analysis as part of her doctoral work. Next, they measured how much the DNA varied within the archaeological samples, in order to determine the number of distinct lineages in each regional population. In a final step, they compared the diversity in past lineages with that found in 379 contemporary salmon samples.

The work confirmed that “there was a lot of genetic diversity present … prior to when Europeans arrived,” Johnson says. Chinook DNA from archaeological samples from the Spokane River, for example, revealed that the river once contained six separate lineages of Chinook, which is more than any single fishery stock held in the contemporary samples. In all, the study, published today in PLOS ONE, revealed that Columbia River Chinook have lost two-thirds of their genetic diversity, whereas the diversity of Snake River fish has declined by one-third.

It is not clear exactly what accounts for the difference between the two basins, or the overall decline. One likely factor has been the dams, but the researchers were unable to retrieve enough salmon DNA from samples archived just prior to the installation of dams to nail down the impact.

The diversity loss could be problematic as fish populations try to adapt to changing river and ocean conditions brought on by climate change and ocean acidification. “The abundance, health, and resilience of salmonids is driven by local adaptations” to specific environmental conditions, says Guido Rahr, Wild Salmon Center’s president and CEO. The question now, says Brian Kemp, an ancient DNA expert at OU and one of the study’s team members: “Is the environment changing faster than these [salmon] can keep up?”