Environmental DNA: Promising new tool is easier on scientists and their subjects

Crime fighters have been using environmental DNA analysis for many years, says Yukon biologist Bruce Bennett.

Crime fighters have been using environmental DNA analysis for many years, says Yukon biologist Bruce Bennett. Today, eDNA sampling techniques, like those that serve police in gumshoes, are helping biologists in gumboots keep tabs on the distribution of species and on habitat health.

Bennett is among the northern eDNA pioneers. “I first heard about it as a member of COSEWIC (Committee on the Status of Endangered Wildlife in Canada) because it had been used to help expand the known distribution of a species known as Rocky Mountain Tailed Frogs,” he says.

“Rocky Mountain Tailed Frogs live in streams in the mountains of the Flathead drainage in southeastern B.C. They are hard to detect – you have to walk in high-energy streams up in the mountains.”

Last fall, Bennett, co-ordinator of Yukon Conservation Data Centre, attended a presentation in Whitehorse on eDNA by Jared Hobbs. Hobbs is a biologist with Hemmera, a B.C.-based environmental consultant firm. In that talk Bennett learned that eDNA was recently used to expand the known distribution of the Rocky Mountain Tailed Frog in southeastern B.C.

The previous distribution had been defined by “eight years of inventory using conventional methods; however, in just five days of survey using eDNA methods, it was discovered that the distribution was actually quite a bit bigger than previously thought,” says Bennett.

This summer, from July 6 to 10, Bennett was part of a team, including Hobbs, that employed eDNA methods in a Yukon biology study. “I think it was the first time eDNA has been used in the Yukon,” Bennett says.

The pilot project targeted the Western Toad (Species at Risk status: special concern) and the Columbia Spotted Frog (Yukon status: imperilled), as well as overall habitat health.

The survey ran from the Annie Lake Road near Carcross to Teslin and Watson Lake, all the way up the South Canol Road to the Nahanni Range Road. The researchers sampled ponds where frogs and toads were already known to exist as well as similar water bodies where they might yet be found.

The Yukon’s eDNA research pioneers were heartened by how non-invasive the procedure was. “We don’t actually handle frogs or toads; we don’t have to clip their toes or anything else to get their DNA,” Bennett says. “Frogs and toads are just naturally sloughing off cells. We don’t have to trample through a whole bunch of habitat to make sure that there isn’t a toad there.”

“Theoretically, you can take a water sample and just say, ‘These are the species that are in this bog.’”

The researchers also recognized the importance of specific cautions. “We have to be very careful that we don’t cross-contaminate one site onto the next,” he says. “So if we actually step in a pond we have to bleach our boots afterwards.” This also ensures scientists avoid transferring pathogens like viruses and fungi.

“There are certain species that can be detected quite well with eDNA, and others that don’t work quite as well,” says Bennett. “The best type of species are aquatic or semi-aquatic ones … things that spend time in the water so you just

sample the water.” Amphibians may move far from home water bodies when they become adults, but all need puddles, ponds, lakes or streams as eggs and tadpoles.

The steps taken by eDNA researchers are pretty straight forward. They begin by preparing a habitat-suitability model. These are built on “points” such as elevation, climate and types local vegetation, says Bennett. With those points scientists can determine which areas are similar to others where the target species – the Western Toad, for instance – is known to breed.

The next step is to “ground-truth” the sites, to see which promising ones actually keep their promises and which don’t. A pond may show up as looking good for all points so far considered, but when scientists arrive, they discover that the water has disappeared or is too cold. Or that a pond bottom is covered by large impenetrable cobbles rather than mud.

Or is there something else in a system beyond the variables the scientists have been using? That’s likely to be a problem in the initial stages of eDNA research here.

“It’s hard to make a good habitat suitability model with very few points,” says Bennett. “We only have about eight sites in Yukon for the Western Toad at the moment. Hopefully, we can add a few more points with this technique, and then use that for improving habitat suitability.”

If a pond looks likely, the scientists will dip a one-litre Nalgene bottle in, fill it and then pour the water out on the shore – three times to make sure there’s no bleach or any other contaminant in the bottle. After the fourth full dip, the bottles are placed on ice, but not frozen, and driven back to a lab. There the contents are pumped through paper filters.

Once a filter is sucked dry, it is slipped into a vial and fixed with an alcohol solution. Then it is shipped to a genetics lab at Washington State University for further processing.

The eDNA researchers are tackling the initial learning curve now – a stage at which any result is a worthwhile learning experience. The hunt is on for false positives and false negatives, and the results of this summer’s pilot project are eagerly awaited.

“First we’ll see if this works, and if it works well we’ll either expand the project or use it for other species,” says Bennett. At a time of climate modification, habitat change and seemingly endless ecosystem cautions, eDNA may help us determine just what is going on among Yukon’s fauna and flora.

And it’s a whole lot cheaper and efficient than trying to radio-collar tadpoles.

For information on Yukon Species at Risk go to www.env.gov.yk.ca/sar

This column is co-ordinated by the Yukon Research Centre at Yukon College with major financial support from Environment Yukon and Yukon College. The articles are archived at www.yukoncollege.yk.ca/research/publications/your-yukon

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