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The New York Times, September 25, 2012

Rare Trout Survives in Just One Stream, DNA Reveals

By Josie Garthwaite

The rare greenback cutthroat trout, Colorado’s state fish, is even more imperiled than scientists thought, a new study suggests. By analyzing DNA sampled from cutthroat trout specimens pickled in ethanol for 150 years, comparing it with the genes of today’s cutthroat populations, and cross-referencing more than 40,000 historic stocking records, researchers in Colorado and Australia have revealed that the fish survives not in five wild populations, but just one.

Stocking records and the tangled genetic patchwork of trout in the southern Rocky Mountain region suggest that efforts to replenish populations were far more extensive and began earlier than previously recognized. Between 1885 and 1953, state and federal agencies stocked more than 750 million brook trout, rainbow trout and cutthroat trout from hatcheries into streams and lakes in Colorado, the researchers found.

The study, published on Monday in the peer-reviewed journal Molecular Ecology as a follow-up to a 2007 study led by the same biologist, Jessica Metcalf, yielded some findings that “may be uncomfortable,” Kevin Rogers, a researcher for Colorado’s state parks authority, said in a call with reporters.

Doug Krieger, senior aquatic biologist for the same agency, Colorado Parks and Wildlife, predicted that the study would shift the direction of conservation efforts.

A shift in the scientific landscape is not an entirely new experience for fish managers working with the cutthroat trout in the region. The 2007 study shook the very foundations of cutthroat trout recovery efforts, showing that managers had accidentally mixed a different subspecies of cutthroat trout, the Colorado cutthroat, with the rare greenback, and then stocked these hybrid strains into otherwise pure greenback streams.

The latest study, whose co-authors also include the biologist Chris Kennedy of the Fish and Wildlife Service and scientists with the University of Adelaide’s Australian Center for Ancient DNA and the University of Colorado, Boulder, shows that the last surviving greenback population lies within a four-mile stretch of a small alpine stream known as Bear Creek. The stream is about five miles southwest of Colorado Springs, on the eastern slope of Pikes Peak.

Located outside the greenback’s native range, this holdout population is probably descended from fish stocked at the Bear Creek headwaters in the 1880’s by a hotelier seeking to promote a tourist route up Pikes Peak, the researchers say.

To map out the historic distribution and range of a species whose taxonomic record is, to quote the latest study, “rife with errors,” Dr. Metcalf sampled skin, gill, muscle and bone from trout specimens collected in Colorado and New Mexico from 1857 to 1889, before the state and federal efforts to propagate and stock native trout were ramped up.

Now housed in museums including the Smithsonian Museum of Natural History and the California Academy of Sciences, the specimens were preserved in ethanol. “The DNA was very degraded, and there wasn’t very much of it,” Dr. Metcalf said. “So this took a lot of effort and repeated sequencing for each specimen.”

Still, ethanol preservation opened a window to the past. “After the 1900’s, a lot of things were fixed in formalin, which keeps them looking the way they were when they were collected,” Dr. Metcalf said. “Before that, things were just straight up pickled” in ethanol.”

The problem for latter-day genetic sleuths is that formalin actually binds with DNA, making the latter impossible to recover. It’s not always obvious what chemicals were used for a given specimen, but the fact that some fish appeared partially decayed was a good sign these trout were preserved the old-fashioned way (in ethanol only), leaving fragments of DNA intact.

“The DNA I get out of 15,000-year-old, extremely degraded animals from Patagonia is in better shape than these ethanol-preserved fish,” she said.

Aside from presenting an approach for using pre-1900 museum specimens to provide a baseline for historic diversity, the study effectively yanks the rug out from under cutthroat trout restoration efforts and raises the stakes in a lawsuit filed last week by the Center for Biological Diversity against federal land managers.

The center claims that “rampant motorcycle use” permitted on trails running along and across Bear Creek is destroying precious habitat. “We’ve asked the forest service to close that trail to motorcycle use and move it,” the director of the organization’s endangered species program, Noah Greenwald, said in an interview.

Even after the construction of bridges and other projects designed to minimize erosion, Mr. Greenwald said, heavy trafficking of erosive soil around Bear Creek causes sediments to fill pools that are vital to cutthroat trout survival.

“It’s a really small stream,” he said. “So the pools are super-important during drought, when the stream freezes in the wintertime, and to hide from predators.”

The Fish and Wildlife Service does not plan to take immediate action around Bear Creek in response to the Metcalf research, which the agency helped finance as a member of the Greenback Cutthroat Trout Recovery Team. Other funds flowed from the Forest Service, the Bureau of Land Management, the National Park Service and Trout Unlimited.

A Fish and Wildlife Service representative told reporters on Monday that the greenback’s status would not be changed from threatened to endangered until a thorough scientific review was carried out and the public had a chance to weigh in. Separate research that the agency will use to crosscheck Dr. Metcalf’s genetic results is to be completed this fall.

Historic records indicate that Bear Creek, like many high-alpine streams made inaccessible by waterfalls and other natural barriers, once had no fish at all. When frontiersmen arrived in the area, they typically would settle near a creek, Dr. Metcalf said., “The first thing you’re going to do is stock it, so you have a good food resource right by your house all year round,” she said,

The revelation that Bear Creek is home to the last remaining greenback cutthroats underscores the importance of protecting the population, said Mr. Greenwald of the Center for Biological Diversity.

“If we can’t protect it, if we don’t do what’s necessary to protect it, “we’re at risk of losing another one of these cutthroat trout subspecies, and that would be a real tragedy,” he said.

This article originally appeared here.

Photo © Paul S. Hamilton