Fall-Run, Spring-Run Chinook Salmon — It’s All in the Genes

A study found that the genetic code of spring-run Chinook salmon, like these in California’s Butte Creek, vary from fall-run salmon only in the DNA variance governing migration times. (Courtesy of Allen Harthorn)

(CN) — A genetic analysis of both spring-run and fall-run Chinook salmon in the Klamath River found they’re essentially the same fish and that only minor deviations separate their genetic codes, according to a study released Thursday.

The different seasonal runs of Chinook salmon have historically been viewed as separate species of fish who leave the Pacific Ocean at different periods to swim up the Klamath and spawn.

That distinction weighs heavy in regulatory regimes for the fish and their habitat, including in the Trump administration’s current review of a petition to extend protections to spring-run Chinook salmon under the Endangered Species Act.

Various populations of Chinook salmon — the nation’s largest species of salmon — are also found in Washington state, Idaho and California. 

A new analysis published Thursday in the journal Science shows that timing of the fish’s migration is determined by a small variance in a section of DNA in their genomes.

The study by University of California, Santa Cruz, researcher John Carlos Garza and colleagues found that Chinook salmon living in a drainage basin like the Klamath River are part of the same population.

Garza, also a research geneticist with the National Oceanic and Atmospheric Administration, said in a statement that genetic variance in salmon is similar to genetic differences in humans. 

“It’s like blue and brown eye color in humans — it just depends on what genotype you inherit from your parents,” Garza said.

Researchers said in a statement released with the study that the findings could aid conservation and management of Chinook salmon if plans to remove dams along the Klamath go through.

The spring-run salmon are the main food source for the Southern Resident killer whales, an endangered population of orca living in the Pacific Northwest.

Scientists sequenced the genomes of 160 Chinook salmon from both the Klamath and Sacramento River drainages and found differences only in genetic codes governing “late” and “early” migration.

Chinook salmon receive two sets of chromosomes from each parent and the DNA variances for early and late migration are called haplotypes.

 Using their new genetic markers for both early (describing spring-run) and late (for fall-run) migration haplotypes, researchers examined 502 Chinook salmon harvested by the Yurok Tribe in the Klamath River estuary.

For salmon with either two early or late migration genotypes, there was no overlap in migration periods, the study found.

Fish with both genotypes, or heterozygous genetic code, overlapped with migration times of salmon with homozygous genotypes.

Garza said in the statement the “extraordinary” finding shows the differences in migrating periods are tied to genotypes, not by what were presumed to be heritable traits for seasonal runs.

“I know of no other gene region that so completely determines a complex migratory behavior in the wild in a vertebrate,” Garza said.

Garza described in the statement how spawning environments affect Chinook salmon populations.

“Spring-run and fall-run fish all start maturing at the same time in the ocean, but during that period after the spring run enters freshwater, they experience different environmental conditions, leading to differences in where and when they spawn,” Garza said. “Also, people notice differences in fat content and body condition because they are encountering spring-run fish earlier in the maturation process than fall-run fish.”

Researchers also found that Chinook salmon were interbreeding after spawning in the Salmon River, a tributary of the Klamath, and often produced spring-run salmon that have fall-run siblings.

“It’s hard to come up with any scenario where you could classify individuals from the same nest as belonging to different populations,” Garza said. “For me, one of the underlying messages is that, in our attempt to categorize things, we’ve overlooked the fact that these are fundamentally the same animal.”

Similar findings surfaced after researchers examined fish carcasses in rivers of Northern California and in the Siletz River of Oregon.

The Chinook salmon haplotypes are the same in lineages across all rivers, indicating that they predate the development of genetic codes tied to specific waters along the West Coast, the study said.

“Those haplotypes are ancestrally the same everywhere, which is good news because it means that there are no variants related to the spring-run migration trait that have been lost with the extirpation of the historically abundant spring run in the upper Klamath River,” Garza said.

Researchers found that Chinook salmon with genetic traits for adapting to the warmer waters of the upper Klamath still spawn in areas around dams that have blocked off full migration routes since 1912.

Spring-run, early migration Chinook salmon spend their summers in deep, cool pools before spawning in the fall. 

“It highlights the importance of taking those dams out, because descendants of the historic upper Klamath spring run are still there — they’ve just lost the (early) haplotype,” Garza said. “Simple crossing with other populations in the Klamath to put the (early) haplotype back into the genetic background of upper Klamath Chinook salmon could restore that spring run.”

Study co-authors include Neil Thompson, Eric Anderson, Anthony Clemento, Matthew Campbell, and Devon Pearse, all with UC Santa Cruz and NOAA, and James Hearsey and Andrew Kinziger of California State University, Humboldt.

Researchers did not immediately respond to a request for further comment.

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