INTEGRATED FLUIDIC CIRCUIT: Scientists at the Columbia River Inter-Tribal Fish Commission (CRITFC) used Fluidigm's 96.96 Dynamic Array to run 96 samples against 96 SNP genotyping assays for a total of 9,216 genotypes on a single chip.
Image courtesy of Fluidigm

Most people would be hard-pressed to tell the difference between Chinook and coho salmon or even between young and old fish. But not the denizens of the Columbia River Basin (particularly in Washington State, Oregon and Idaho): they not only know their salmon, but their ability to distinguish between species is key to preserving the fast-disappearing fish.

Salmon, once plentiful in the Columbia River, are now a dying breed—a situation that threatens not only their existence but the livelihood of folks inhabiting the mighty river's shores: The commercial fishing industry employs more than 3,600 people and generates more than $100 million annually in Idaho, Oregon and Washington alone, according to a 2005 report by the Northwest Power and Conservation Council in Portland, Ore. Salmon are also an important part of Native American tribal ceremonies.

But overfishing, hydroelectric dams and development (leading to habitat destruction) have taken a toll on the coveted fish in the Columbia, where its annual migrating population has plummeted by as much as 90 percent since its peak in the 19th century—when it is estimated to have been as bountiful as 20 million—to numbers as low as a few million in some areas. Construction of hydroelectric dams along the Columbia and its tributaries beginning in the early 1900's boosted power production but also winnowed the salmon population to about 3 percent of the levels they were when Lewis and Clark journeyed through the area more than 200 years ago.

In an attempt to reverse the decline, local Native American tribes comprising the Nez Perce, Umatilla, Warm Springs Reservation and Yakama in 1977 established the Celilo Fish Committee, which has since been expanded and renamed the Columbia River Inter-Tribal Fish Commission (CRITFC).

Over the past decade, the CRITFC has used genetic analysis to study local fish populations, which includes Chinook, sockeye and coho salmon. The goal, says Shawn Narum, CRITFC's lead geneticist, is to help increase the salmon population by pinpointing the breeds at risk and working (alongside local fish hatcheries) to replenish the most needy ones. "As [human] impacts to natural populations steadily increase, a better understanding of the rate and level of species' adaptability [is] necessary," he says.

CRITFC includes about 60 geneticists, hydrologists, fish biologists, biometricians, meteorologists and other scientists (plus a support staff of about 500 people) dedicated to studying salmon and their ecosystem. Determining the genetic variations in (and developing genetic signatures for) Columbia River Basin salmon populations helps the researchers better understand the fish's diversity, adaptation and dispersion. These genetic signatures may also be used to identify when previously unknown salmon species migrate to the area.