Fishing in the gene pool

Conservation genetics yields new sculpin species in Montana and Idaho

This story was published by High Country News, National Geographic’s Water Currents blog, and the Missoula Independent.


The cedar sculpin, or Cottus schitsuumsh, named by the Coeur D’Alene Tribe. Schitsu’Umsh (pronounced s-CHEET-sue-umsh) refers to the tribe itself and means “Those who were found here.” Illustration by Emily Harrington.

One day last summer, Michael LeMoine, a Ph.D. candidate in fisheries biology at the University of Montana, carried a nondescript cardboard box into the Missoula FedEx office. Inside it was a jar of ethanol containing a single specimen of a new species of sculpin.

The woman at the counter asked LeMoine for the value of the contents. He hesitated, considering. “My trouble, ma’am,” he remembers answering, “is that you don’t know this, but this is a new species in this box, and I really have no idea what the value of it is.”

So LeMoine hazarded $10,000, an amount that didn’t include the value of the months of field and lab work it took to identify the fish. Nor could he begin to answer the unspoken philosophical question: What is the value of a species?

FedEx charged $5 to insure the package.

“Five bucks to insure a new species,” LeMoine says. “If only that would work in the real world.”

In January, Zootaxa, a taxonomy journal, published LeMoine and his colleagues’ description of the cedar sculpin, or Cottus schitsuumsh, which is found only in parts of the upper Columbia River Basin in Montana and Idaho. Of the hundreds of sculpin species around the world, several are abundant in the cold freshwaters of the Pacific Northwest, where they are tasty prey for salmon and trout and play a crucial role in stream ecology. They’re strangely colored, odd little bottom-feeders with unflattering names like “slimy” and “spoonhead.” LeMoine describes them as “a frog head connected to a slug with some fins on it.”

The problem is that all sculpins look alike, to such a degree that biologists consider them one of the most difficult groups of freshwater fish to identify. LeMoine and his colleagues identified the cedar sculpin by scanning a short sequence of its DNA. In doing so, they demonstrated how this decade-old taxonomic tool, known as DNA barcoding, can help biologists discover new fish species—or distinct populations—within what was thought to be a single, undifferentiated species. The researchers, among the West’s pioneers in the fast-growing field of conservation genetics, which studies the variability of genes in species and uses that information to help preserve them, have already shown that there are probably even more new sculpin species out there—along with who knows what else.

By applying genetic techniques to fish and amphibians, says Michael Young, a co-author of the paper, “it’s quite likely that we’d encounter something that’s extraordinarily rare.” In the process, they could identify new species that are already on the brink of extinction, thereby joining discovery and preservation.

Young, a fisheries biologist at the U.S. Forest Service’s Rocky Mountain Research Station in Missoula, led the team that discovered the new sculpin. He describes his research as “quantifying biodiversity,” mapping all the fish and amphibians in the Rocky Mountain West’s river basins. Doing this, he says, will set a benchmark, a standard of comparison for monitoring the future effects of climate change on species. It’s an ambitious effort that involves gathering thousands of samples over vast landscapes.

Young and his colleagues started with sculpins because they presented a “target of opportunity”—since they’re hard to distinguish with the naked eye, distinct species have probably been lumped together. Between 2008 and 2011, Young’s team collected sculpins from 398 streams in northern Idaho and western Montana. DNA barcoding revealed that as many as eight could be genetically distinct, as-yet-unnamed species.

The most distinct, it appeared, was a sculpin found in Idaho’s Coeur d’Alene and St. Joe rivers and a couple of Clark Fork tributaries west of Missoula. But a unique gene sequence alone does not establish a new species; it must be combined with unique morphology. Young tasked LeMoine, his student, with finding those physical differences, however slight.

This genetic outlier had been considered a shorthead sculpin, or Cottus confusus, which, as University of British Columbia biologist J.D. McPhail once noted, “aptly describes its taxonomic history—confused!” Differentiating between shorthead and other sculpin species had confounded biologists for decades. As LeMoine waded into the murky taxonomy, the assignment was made even more difficult by the sorry state of the region’s natural history archives, which offered few specimens for comparison.

Ultimately, Don Zaroban, the curator of fishes at the College of Idaho’s Museum of Natural History, helped LeMoine uncover a key distinction: The species that would eventually be named Cottus schitsuumsh has a single, small, skin-covered protrusion on its preopercular bone, located between the cheek and gill cover, whereas all other sculpin in the region have two. The difference is visible only through dissection.

LeMoine, Young and the four other co-authors of the species description posit that the cedar sculpin’s irregular distribution is the result of “bucket biology.” “We think somebody introduced it into Montana—probably fishermen—and it invaded rather broadly within those basins and completely replaced the native sculpin there,” Young says, “and nobody knew it was happening.” The Coeur D’Alene Tribe, in whose ancestral homelands the sculpin was discovered, named it. Schitsu’Umsh (pronounced s-CHEET-sue-umsh) refers to the tribe itself and means “Those who were found here.”

Young and fellow researchers are now applying DNA barcoding to other fish, such as the westslope cutthroat trout, Montana’s state fish. Despite the threat of habitat loss and hybridization with rainbow and Yellowstone cutthroat trout, the U.S. Fish and Wildlife Service has declined to protect the westslope cutthroat under the Endangered Species Act. By collecting specimens from across the species’ entire range and analyzing their DNA, Young’s team could very well find evidence of a new trout species or at least genetically distinct populations. Either would bolster the scientific argument for listing, since divided populations result in smaller and more vulnerable ones.

Once the trout’s genetics are understood, Young says, it may be possible to help it cope with climate change. Genetically unique stocks of the fish would have different evolutionary histories; some may have been selected for dealing with warmer climates. “If we want to move some fish,” he says, “those might be really good ones to move because they’re likely to be more resilient to climate change than other forms that only deal with really cold environments.”

Genetic sleuthing offers intriguing possibilities, but also underscores how much remains to be discovered. As freshwater biodiversity continues to decline, we’re likely losing species we’ve never even named.