New genetic evidence could have major implications in the fight to save spring-run Chinook

Video: Fight between tribes and farmers over Northern California’s water

Northern California's Yurok and Hoopa Valley tribes thrive on the salmon population in the Klamath River. With water levels getting lower, they are doing everything possible to preserve the river's strained ecosystem and to prevent another histori
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Northern California's Yurok and Hoopa Valley tribes thrive on the salmon population in the Klamath River. With water levels getting lower, they are doing everything possible to preserve the river's strained ecosystem and to prevent another histori

A study published Wednesday by researchers at UC Davis may have major conservation implications for salmon in California and the Pacific Northwest. The study provides new evidence that “springers” and other salmon that migrate upstream from the ocean to spawn early in the year are genetically different than later migrating populations.

This evidence could be used in the fight to protect groups of steelhead and Chinook salmon in Northern California and the Pacific Northwest. An earlier petition by conservation groups to list them under the Endangered Species Act in 2011 failed because it wasn’t clear that the groups were distinct.

Across the Western states, several salmon populations are listed under the Endangered Species Act, including Central Valley spring-run Chinook in the Sacramento River and tributaries upstream.

For the steelhead and Chinook species of Pacific salmon, some populations migrate earlier in the season. This group of “premature migrators” leave the ocean to travel upstream before their sexual organs mature and while the snowmelt-fed flows are receding. They migrate farther upstream than their counterparts and wait in cool freshwater pools until they reach sexual maturity and spawn around the same time as the late runners that migrate as sexually mature adults.

These premature migrators, spring-run Chinook and summer steelhead, are special. For one, they’re fattier, and are valued for their taste. But these populations have also suffered drastic declines across their range and haven’t fared as well as the later migrators.

The work, published in the journal Science Advances by Michael Miller at UC Davis and collaborators at other institutions, examined the genetics of these salmon populations and may have wide-reaching implications for conservation decisions on imperiled groups of many species.

The researchers looked at the DNA from hundreds of steelhead and Chinook salmon that migrated to streams in Northern California and Oregon. Using a sensitive genetic technique, they surveyed hundreds of thousands of points on the salmon DNA to compare the premature and later migrators.

For steelhead and Chinook salmon, they found that one location on one gene correlated strongly with early migration. This went against the prevailing view that locations on multiple genes are responsible for this trait. If multiple genes play a role in early migration, it seems more likely that the trait evolved at different times and ways in these groups.

Based on their result, the researchers think that this one gene instead evolved a long time ago, independently in steelhead and Chinook, and may have been a rare event.

“This means that the existence of spring Chinook and summer steelhead depend on a specific version of the gene, and this version cannot be expected to easily re-evolve if lost. For example, if premature migrating fish are lost, that gene version will be lost and may take many thousands to millions of years to re-evolve,” said Miller in an email.

Their finding also brings new urgency to the fight to conserve these salmon by Native American tribes in Northern California, including the Karuk and Yurok.

“We’re having the worst year ever in history on the Klamath when it comes to salmon,” said Craig Tucker, Natural Resources Policy Advocate for the Karuk Tribe.

In a river that historically had runs of millions of fish, the Karuk only expect about 10,000 Chinook salmon this year, Tucker said.

“The tribal people, the Karuk in particular, have been saying this all along that these are different fish. There’s a different word for them in the Karuk language. They taste different. They play different roles ceremonially. So I think, from the tribe’s perspective, Western science is catching up to traditional knowledge,” Tucker said.

Miller also has a personal connection to the salmon.

“I grew up in Western Oregon and have always been fascinated by salmon and steelhead. I’ve spent a lot of time salmon and steelhead fishing since I was a kid,” said Miller by email. “My dream was always to apply my genetics skills to salmon conservation … fortunately, multiple technological advances, including some that I was involved in developing, allowed me to achieve that research goal,” he said.

The science is sound, said Robin Waples, a senior scientist at NOAA Fisheries who also studies the genetics of Pacific salmon populations.

Miller’s use of this genetic technique allowed him to see these differences in the salmon genome that have escaped previous attempts.

“It’s sort of like a needle in a haystack … and it’s only though this very exhaustive search that they found something,” he said.

But Waples isn’t sure about the study’s conclusions for conservation. Specifically, he wants to see more evidence that this trait only evolved once and that the genetic code that carries it isn’t out there in populations that run at a time between groups studied here.

“But there’s no question that this potentially has important implications for conservation and management. It does not automatically mean that the current framework is not adequate. But it does suggest it’s important to have a careful look at the current framework and see if it is robust in light of these new findings,” Waples said.

Wednesday, Nov. 2, 2016, was the first day the fish ladder at Nimbus Fish Hatchery was opened for the fall run of Chinook salmon, giving those impressive fish some important help in successfully going through their life cycle.

Carolyn Wilke: 916-321-1073, @CarolynMWilke

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