WSU researchers compared DNA from ancient fish bones to modern chinook and found a dramatic decline in genetic variability.

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Fish bones unearthed from prehistoric trash heaps in the Pacific Northwest reveal a dramatic decline in the genetic diversity of chinook salmon, an iconic species that once thronged the region’s rivers and streams.

Today, many chinook stocks across Washington and Oregon are threatened or endangered, and scientists have long suspected that their genetic variability has suffered as well. But a new analysis from researchers at Washington State University is the first to directly measure that loss — thanks to those old bones and advances in DNA extraction.

“Genetic technology is moving so fast, it finally caught up to where you can actually get DNA from these ancient bones,” said Bobbi Johnson, a recent doctoral graduate who spent six years on the project and processed more than 700 samples.

She and her colleagues found that chinook from the upper Columbia River have lost as much as two-thirds of their genetic diversity, while variation among fish from the Snake River has dropped by about a third. Another way to express it is that the number of distinct linages, or genetic families, has declined by those amounts, Johnson explained.

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While not surprising, the results are exciting, said University of Washington fisheries biologist Thomas Quinn, who wasn’t involved in the research.

“This study provides a new perspective and a new type of information to help us assess the effects of human activities on these salmon,” he said.

Genetic diversity is important, because it helps protect species against disease and environmental change. “If you lose genetic diversity, you lose that buffer,” Johnson said.

The study, published Jan. 10 in the journal PLOS One, was not able to pinpoint the exact cause of the genetic depletion, though there are only two main suspects: Fishing and dams.

Native Americans fished for chinook for over 9,000 years before European settlers ratcheted up the pace dramatically beginning in the 1860s. Between 1889 and 1922, harvests were as high as 25 million pounds a year.

It’s possible chinook were already genetically depleted by the time dam construction started in the 1930s, Johnson said. If not, then it’s likely the dams were the main culprit.

“The thing people want to know is the why, but that’s the piece we don’t have,” she said. “All we can say is: This is what chinook looked like a really long time ago.”

The fish bones that opened the window onto the past were found in archaeological collections held by the Confederated Tribes of the Colville Reservation, the Spokane Tribe of Indians and WSU.

Mostly vertebrae gleaned from trash piles, the bones were often sitting in dusty boxes in basements, Johnson said.

The samples ranged in age from 1,100 to 7,500 years old.

To extract DNA, Johnson applied similar techniques to those used in recent years to coax minute bits of genetic material from Neanderthal bones and the 9,500-year-old skeleton called Kennewick Man. Johnson’s target was DNA from cellular organelles called mitochondria, which is much more abundant than DNA from the nuclei of cells.

To avoid contaminating her samples, Johnson wore two pairs of gloves, hair nets and freshly bleached lab coats. The work area was meticulously scrubbed and disinfected with bleach. Even so, only 84 of 346 ancient bones yielded usable DNA.

The 379 tissue samples collected from fish swimming today in the Columbia and Snake Rivers were much easier to work with — and much less nerve-wracking.

“With modern samples, you can always get more,” Johnson said. “With the ancient bones, there’s no room for error.”

The researchers were surprised to see such a difference between the Columbia and Snake River systems, Johnson said.

Both basins were subject to heavy fishing and the dams on the Columbia affect the entire region.

There are now more than 400 dams across the Columbia River system, the researchers wrote in the journal article, blocking more than half the spawning habitat. The Columbia River is inaccessible to salmon above Grand Coulee Dam. The only remnant of the chinook that once spawned in the upper river are small populations that were trapped and transplanted to the Entiat, Wenatchee and Methow Rivers in the 1940s, Johnson said.

To answer the question of whether fishing or dams were most to blame for the genetic losses, scientists would need preserved tissue samples or fish bones from the late 1800s through the mid-1900s. They tried to extract DNA from specimens in formaldehyde at the UW’s fish collection, but failed, Johnson said.

They even briefly considered a search for mounted fish trophies, but weren’t sure they would yield good DNA.

“Specimens (from that time) might exist, but they don’t seem to be in museums,” Johnson said. “Maybe somebody has them.”