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Even Elusive Animals Leave DNA, and Clues, Behind
New York Times, January 22, 2015

You wouldn’t think hellbenders would be hard to find: The huge salamanders, the biggest amphibians in North America, can grow up to 30 inches long. Yet hellbenders make themselves scarce, living on the bottoms of mountain streams, lurking under massive rocks.

As a result, locating hellbenders takes a crew of scientists. First, some of them must wedge a long pole under a rock to hoist it up, and then their colleagues must plunge into the chilly water to catch their quarry.

A couple of years ago, Stephen Spear, a conservation scientist at the Orianne Society in Athens, Ga., heard about a possible alternative. Instead of finding rare animals, some experts were gathering animal DNA from their habitats. That way, they didn’t have to track down a species to be sure it was there.

Dr. Spear decided to try. He traveled to rivers in the Southeast where he and his colleagues had found hellbenders, and scooped water into jugs.

One day on the banks of the Clinch River in Tennessee, Dr. Spear met fishermen curious about what he was up to. Looking across the broad river rushing by, he explained that he was trying to catch a few bits of genetic material from a single hellbender lurking under a distant rock.

“You just felt silly,” Dr. Spear said. “I won’t lie. I wasn’t convinced it would work.”

Despite his doubts, Dr. Spear and his colleagues analyzed the water for traces of hellbender DNA. As they reported in the journal Biological Conservation, it was there.

“Essentially, everywhere that we know that they’re there from past surveys, we’d pick them up,” Dr. Spear said. Outside the hellbender’s range, the scientists failed to find any of its DNA, making contamination an unlikely explanation for their results.

“I converted pretty quickly,” Dr. Spear said.

He is not the only convert. Over the past few years, scientists have found DNA that many animals shed in their surroundings. These genetic signatures provide valuable clues, helping researchers track invasive species moving into new territories and endangered animals flirting with extinction.

Eventually, it may be possible to estimate the population of a species in a habitat simply by measuring how much DNA they leave. And instead of toting up hellbenders or other elusive critters, scientists may be able to catalog much of the diversity in animals and plants in a particular ecosystem simply by collecting DNA.

The first scientists to gather environmental DNA were microbiologists taking advantage of the universal abundance of microbes. A single spoonful of soil harbors a billion bacteria, for example, each packed with DNA.

Then zoologists started isolating animal DNA from hair and fresh feces. Still, they considered it very rare for animal DNA to survive for long in the environment on its own.

In recent years, that assumption has been proved wrong.

Eske Willerslev, a pioneer in environmental DNA at the University of Copenhagen, and his colleagues ran a series of experiments that showed environmental DNA can give zoologists a reliable snapshot of the animals in a particular place. In zoos, for example, they dug deep into the dirt and found DNA matching that of the elephants, lions and other animals living in each enclosure.

Dr. Willerslev and his colleagues also investigated lakes and other bodies of water, discovering that animal DNA could survive at detectable levels for weeks. Their methods were so sensitive that they found DNA from deer that had drunk at the edges of ponds.

For zoologists, these results were a breakthrough. “In the past three years or so, the field has completely exploded,” Dr. Willerslev said.

The standard methods for counting animals can be expensive, time consuming and limited. To survey salmon, for example, scientists typically build traps known as weirs to catch fish as they swim upriver to spawn. But in the raging waters of spring, most salmon may slip by, swimming into streams stretching across vast watersheds.

Matthew B. Laramie, an ecologist with the United States Geological Survey, studies the chinook salmon that live in northern Washington State. After learning of some early successes with environmental DNA, he decided to look for chinook DNA across hundreds of square miles of streams and rivers.

Like Dr. Spear, he started out a skeptic. “I had my doubts,” he said. “These rivers are swollen with a lot of water, a lot of debris.”

But as Mr. Laramie and his colleagues reported in Biological Conservation, they found chinook DNA in most of the places where they knew the fish were, and didn’t find it in most places where these salmon had not been found.

Mr. Laramie expects that environmental DNA will become useful for tracking the spread of salmon now returning to parts of their historical range. Scientists should be able to follow them as they recolonize streams and rivers.

And other researchers will be able to borrow the methods that he and others are developing to study other fish. “They can kind of take it and run,” Mr. Laramie said.

Environmental DNA can help scientists track unwanted animals, too. Detecting invasive species is crucial for efforts to control them, but conventional methods aren’t always adequate. Antoinette J. Piaggio of the National Wildlife Research Center and her colleagues have found that Burmese pythons in Florida wetlands are leaving detectable DNA, which may be helpful in following their alarming spread.

Environmental DNA can provide important clues about species in decline, as well. It is hard for scientists to decide when to declare a species officially extinct, since a few stragglers may still survive unseen. But even these hard-to-find animals shed DNA, a signal to scientists that the species survives, if barely.

Researchers still need to learn more about how DNA survives in the environment before these new methods can stand on their own, Dr. Willerslev said. But he was optimistic that environmental DNA would begin providing more clues to zoologists about the animals they study, such as population sizes and the diversity of species in a particular ecosystem.

Those hopes may seem far-fetched. Then again, so was the notion that genetic traces of a deer might linger for weeks in a pond from which it drank.

Copyright 2014 The New York Times Company. Reproduced with permission.
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