eDNA Surface Sampling Reveals Surprising Chinook Migration Patterns

Using new eDNA sampling technology, scientists at the Northwest Indian Fisheries Commission have uncovered Chinook salmon in remote headwaters, reshaping fisheries conservation and restoration strategies.

In Washington’s remote Queets River, new technology is finding what the human eye cannot see.

Accessible only by helicopter and wading waist-deep before an extreme headwater, few people have ever stood at the Olympic National Park waterfall where ecologist John Hagan and his team at the Northwest Indian Fisheries Commission (NWIFC) recently captured surprising new scientific data. What reshaped their understanding of Chinook salmon was not in what they saw, but what the DNA in the water revealed.

Hagan’s team deployed Ocean Diagnostics’ portable eDNA Surface Sampler to collect genetic material in areas too remote and extreme to obtain with existing tools. These samples, analyzed back in the laboratory, revealed Chinook salmon in a location historically believed to be beyond their migratory reach. This data supports tribal fisheries managers in understanding how human activities may be altering salmon behaviour across the Pacific Northwest and introducing conservation and restoration activities to protect them.

eDNA surface sampling for salmon detection

Salmon are a cornerstone species of coastal ecosystems, Indigenous food systems and regional economies, but global populations continue to decline due to warming waters, habitat loss, barriers to passage and cumulative human pressures.

Traditional fish surveys, like visual observation, netting or electrofishing, can miss species in remote headwaters, wetlands and obscure tributaries. Environmental DNA offers a different approach.

The portable and battery-powered eDNA Surface Sampler works by pumping and filtering water in the field to collect trace genetic material shed by organisms, allowing scientists to detect species presence without ever seeing the fish themselves.

“It’s really exciting to get the data back from the lab and see in really high definition what we didn’t see with our eyes when we were there,” Hagan said.

Collecting reliable data, even with existing eDNA sampling tools, is challenging, particularly in remote or extreme places. New technologies significantly reduce logistical barriers to collecting samples in extreme environments.

Hagan illustrates, “The eDNA Surface Sampler works really well in both pack rafts and larger boats that we use on lakes. We also use them quite a bit for roadside sampling. You can just kind of get out into the middle of a wetland and stick your filter over the side, hit the button and sit there writing in your field notebook. It's nice to have that flexibility.”

Scaling eDNA sampling for fisheries management

NWIFC supports 20 tribal fisheries managers who undertake some of the largest-scale restoration and monitoring projects to map fish distribution and watershed dynamics and create better salmon habitat. The Commission first began using eDNA in 2018 to study mud minnows, a very tiny freshwater fish that only exists in Western Washington.

These minnows occupy small channel wetlands, making them very difficult to catch and study, but they are key indicators of traditional habitat health critical to Indigenous peoples. eDNA enabled the team to detect them in a few spots and successfully monitor them over time, where conventional methods failed.

Today, NWIFC monitors multiple species in 1,300 freshwater sites across Western Washington, including wetlands and remote headwaters like the Queets, using eDNA methods with the Surface Sampler.

“It was exciting for us to know that the same path we travelled up this Canyon and through all these small waterfalls, the Chinook were there with us the whole time. Being in this magical little Canyon, we were sharing that space with these incredible fish that had a much more difficult time getting up there than we did,” Hagan reflects.

eDNA surface sampling advances salmon recovery and conservation

By revealing hidden patterns of fish movement and habitat use, environmental DNA is giving tribal fisheries managers a clearer, data-driven foundation for protecting one of the Pacific Northwest’s most critical species.

As Hagan explains, “(eDNA) enables the collection of multi-marker data, which is incredibly mind-blowing. We’re getting community composition information and food web dynamics.”

The NWIFC’s ever-growing eDNA dataset supports 20 tribal fisheries managers to:

• map fish distribution at the watershed scale
• track shifting salmon baselines over time
• create an accurate index of occupancy across the landscape
• identify priority habitats for restoration
• inform land-use, culvert replacement and fish passage decisions
• and detect invasive species and monitor rare or endemic fish
  

“The larger this data set grows, the clearer the story becomes,” says Hagan. “It’s not always a happy story, but it informs really important work.”

Learn more about eDNA Surface Sampling here.

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