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Some Chinook salmon return to freshwater rivers in the spring, but others migrate in the fall.

Mark Conlin Visual&Written/Newscom

Salmon study sheds light on why fall-run fish are bigger than their spring-run cousins

For the Yurok people, who have lived at the mouth of the Klamath River for generations, the spring run of Chinook salmon (Oncorhynchus tshawytscha) is a welcome—and nutritious—relief from winter. But as the fish have dwindled to just a fraction of their original numbers, Indigenous groups there are pushing to have them protected by the Endangered Species Act. New research, which suggests genes play only a small role in distinguishing the spring salmon from their fall-run cousins, may call into question the need for such a designation.

The rivers of the Pacific Northwest used to teem with two waves of Chinook: those that arrived in March or April, and those that came 6 months later, swimming from the sea to their upriver breeding grounds. Although technically the same species, the spring-run and fall-run fish have some “iconic differences,” says Eric Anderson, a molecular geneticist at the National Oceanic and Atmospheric Administration’s Southwest Fisheries Science Center. Spring salmon are smaller, fattier, and less sexually mature than fall fish. They also swim further upriver to breed.  

To tease out the genetic basis of those differences, Anderson and colleagues teamed up with Yurok fishers living at the mouth of the Klamath River in northern California. Together, they examined 500 fish as they started their upstream journeys in all four seasons. The researchers measured the size of each fish, assessed its fattiness and reproductive status, and took samples of its DNA. The researchers gathered similar data from other rivers.

Past studies have shown that a small region of the salmon chromosome 28 contains two genes, GREB1L and ROCK1, that vary between spring and fall salmon. Anderson and his colleagues did further genomic studies, sequencing the whole genomes of 160 fish in the hopes of linking the two genes to the spring and fall traits. The data set is “impressive” and the work unique says Sheela Phansalkar Turbek, an evolutionary biologist at the University of Colorado, Boulder, who was not involved with the work.

The researchers found that, although spring-run fish had one version of the genes and fall-run fish had another, the genes had nothing to do with how fat or mature the salmon were, they report today in Science. Instead, the team concludes these differences exist because fall-run salmon are measured months after the spring salmon, giving them more time to fatten up in the ocean. “The cool thing about this paper is it shows that a lot of differences can be explained by timing,” says Michael Miller, a geneticist at the University of California, Davis, who helped pin down the variant genes, but was not involved with the new work. “There’s a whole cascade of effects that come from [simply] changing the timing.”

The new data also show that fall-run and spring-run salmon often interbreed, Anderson says. DNA analyses—and data from migrating fish—reveal that hybrids usually begin their journeys between spring and fall, often in the middle of summer. And a computer simulation in the new study suggests interbreeding occurred long before humans modified the riverscape with the dams that prevent many spring salmon from reaching their upriver breeding grounds. “It’s been a long ongoing natural process of gene exchange,” Anderson says.

In some ways, this work challenges the idea that the two fish should be categorized and managed separately, Turbek says.  Some researchers have proposed that spring-run fish might re-emerge from the population of hybrids or from spring-run salmon introduced from other rivers. But others are concerned that such efforts could falter—or introduce new diseases to the environment. It’s “not the sort of thing we can count on,” Miller says.

He also thinks interbreeding has risen sharply in recent years because of dams and other human modifications to rivers that make it more likely that spring-run and fall-run salmon breed in the same pools. As bigger fall-run fish outcompete spring-run fish, those early arrivers—and their version of the gene that dictates migration timing—may disappear. “Spring salmon are headed towards extinction in the Klamath and practically every other watershed in Pacific Northwest,” says Craig Tucker, an independent biologist and consultant to the Karuk Tribe, which petitioned to have spring-run salmon protected.

Tucker is concerned this new study is “muddying the scientific waters” and could slow the process of getting protection for these salmon. Miller agrees. But Anderson says the true strength of the work is that it shows the importance and uniqueness of the spring-run genes, and not just in the Klamath River. “It stresses that they should be conserved throughout the species.”

*Correction, 29 October, 4:15 p.m. In the initial version of this story, the wrong tribe was identified as living at the mouth of the Klamath River and working with these researchers.