A team of researchers working on a project funded by the U.S. Geological Survey’s (USGS) Alaska Climate Adaptation Science Center (Alaska CASC), in collaboration with the USGS Alaska Cooperative Fish and Wildlife Research Unit, is testing a new tool for tracking Chinook and chum salmon runs with greater reliability and resilience to high streamflow events.

The research is led by Jeff Falke, Erik Schoen and Andrés Lopéz. Falke is Unit Leader of the Nevada Cooperative Fish and Wildlife Research Unit at the University of Nevada, Reno (previously of the Alaska Cooperative Fish and Wildlife Research Unit). Schoen and Lopéz are both faculty members at the University of Alaska Fairbanks.

“Our objective is to assess whether we can use environmental DNA (eDNA) as a tool for determining salmon run timing and abundance in five Yukon River tributaries,” explains Maggie Harings, a graduate research assistant at the University of Alaska Fairbanks.

Each spring, millions of salmon begin their epic migration from the ocean to their spawning grounds upriver. On the Yukon River in Alaska, salmon can travel up to 1,800 miles – all without eating – navigating one of the longest migration routes in the world. Imagine running from New York City to Denver without snacking. These annual salmon runs are critical food sources for wildlife and Alaskan communities who have depended upon subsistence fishing for generations, as well as prized fishing grounds for anglers from around the world. However, salmon numbers are dropping, prompting many regulatory restrictions to conserve stocks and a need for reliable monitoring.

Tracking salmon migrations across such vast distances is labor and time intensive and requires a bit of luck. Researchers invest large amounts of time and effort to monitor salmon abundance, hoping that river conditions will allow them to count the fish as they return to their spawning grounds. But with climate change shifting both river conditions and salmon populations, managing and monitoring these populations is becoming increasingly difficult.

As climate change brings more extreme weather and frequent high-water events, traditional monitoring methods like weirs and sonar are unreliable, as equipment cannot be safely left in the rivers or salmon can pass through assessment sites without being counted. eDNA offers a potential solution to these monitoring disruptions. By collecting water samples and analyzing traces of DNA left behind by the salmon as they swim upstream, researchers can gather information about salmon abundance without needing to directly observe or handle the fish.

For the project, the research team collaborated with technicians at observation sites across the five tributaries and trained local collaborators to collect daily eDNA samples during normal salmon count activities. Once collected, the researchers can analyze the eDNA data alongside daily salmon counts, looking for patterns where a certain amount of DNA corresponds to certain numbers of fish.

A key part of Harings’ research was learning how to isolate salmon DNA from the samples, of which she and her collaborators have collected more than 800 over two years. Environmental samples from thriving ecosystems, like robust river tributaries, contain genetic material from all kinds of organisms, so the researchers need to isolate salmon-specific DNA. Harings has spent hours in the lab figuring out the right assays to ensure they are quantifying the right species-specific DNA.

While eDNA is often a reliable tool for determining if fish are present, Harings acknowledges that using it to estimate population sizes can be tricky: “Part of my work is to refine the sampling methods and to test different conditions to try and parse out meaningful data about population sizes,” she says.

Environmental factors like streamflow and temperature can affect how much salmon DNA gets collected, so it isn’t as easy as just quantifying it. Based on some preliminary data, timing matters too, as eDNA concentrations increase as more salmon migrate upstream of sampling sites.

“But even if the data are qualitative – like determining whether it was a good or bad year for salmon – it can still provide valuable insights.”

Project collaborators, including the Alaska Department of Fish and Game, U.S. Fish and Wildlife Service, and the Tanana Chiefs Conference, are excited about this new monitoring technique. Analyzing eDNA has the potential to save a lot of time and labor, and to monitor salmon in remote locations where there is no established monitoring equipment. eDNA is unlikely to replace traditional methods like weirs or sonar, but it could be an extremely valuable addition to the toolbox, particularly during periods of high river flows.

“Our goal is to ensure that communities on the river have the tools they need to protect their heritage and livelihoods,” Harings explains.

The ONB features articles from Cooperative Fish and Wildlife Research Units across the country. Working with key cooperators, including WMI, Units are leading exciting, new fish and wildlife research projects that we believe our readers will appreciate reading about. This article was written by Shannon Bayliss, USGS National Climate Adaptation Science Center, and Oak Ridge Science and Education (ORISE) Research Participant.