January 3, 2019 — Scientists have published a novel method for counting Pacific salmon – analyzing DNA from the slime the fish leave behind in their spawning streams.
The study, funded by The National Geographic Society, is published in the journal Molecular Ecology Resources.
“When we analyzed the environmental DNA sloughed into water from salmon tissues, including mucus and skin cells, we got very accurate counts,” said Taal Levi, an ecologist at Oregon State University and lead author on the study. “This is a major first step for more informed salmon management decisions because it opens up the possibility to affordably monitor many more streams than the few that are currently monitored.”
Pacific salmon are a keystone resource in the Pacific Northwest, with an economic impact of well over $500 million each year in Alaska alone. Currently, spawning salmon are counted at just a few streams due to the reliance on human counters, or in rare cases, sonar. Five species of Pacific salmon – pink, chum, sockeye, coho, and chinook – are distributed through more than 6,000 streams in southeast Alaska alone. More than 1,000 of those streams host spawning salmon.
Salmon are anadromous: They migrate from home streams to the ocean as juveniles, and return a few years later as adults to spawn. Anadromous fish such as salmon provide a straightforward scenario for testing whether environmental DNA (eDNA) can be used to count fish, because large numbers of salmon release their DNA as they pass a fixed sampling point, either as they swim up a river or stream as inbound adults or swim downstream as outbound juveniles.
In many rivers and streams, including the majority of freshwater systems in Alaska, adult salmon returning to spawn are poorly monitored, as are fry and smolt production resulting from spawning salmon.
For the study, researchers collected water samples in 2015 and 2016 near the Auke Creek research weir, nearly 16 kilometers north of Juneau. Weirs consist of a series of closely spaced bars across an entire stream to prevent the passage of salmon, except through a single, narrow gate over which a human observer tallies and identifies salmon as they file through.
The Auke Creek weir, cooperatively operated by the National Marine Fisheries Service, in collaboration with the University of Alaska and the Alaska Department of Fish and Game, is known as one of the most accurate fish counters in the world, Levi said.