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The Clues In The Water

The Clues In The Water

How environmental DNA is showing us all of the life we cannot see
By Jimmy Thomson
Jul 17
From the July/August 2018 Issue

Cascading down every stream and river, and swirling in every tide, is a wealth of information. Scoop up a handful of that water and it can tell you what fish are spawning upstream; what larvae are digging in amongst the pebbles to moult; perhaps even what large, hoofed animal has taken a drink nearby, spilling saliva and flecks of skin into the water.

Tiny particles of fur, scales, feces, urine, sperm, eggs, mucus—all of these minuscule traces of life—contain DNA. And that DNA is ushering in a revolution in what we can tell about our environment. Through a technique known as environmental DNA monitoring (or eDNA) scientists can document the creatures living in or near water without ever seeing or disturbing them. The process relies on water samples, which are analyzed for DNA and checked against a growing database of wildlife profiles to create a detailed picture of an area’s ecosystem.

It’s a new technique, so the potential is dampened by uncertainty: to be useful, it needs to be trusted. Robert Bajno, a Winnipeg-based biologist at the Department of Fisheries and Oceans, has spent five years trying to work out how best to apply the technology across Canada. He and others at DFO have been conducting field studies to validate it and its processes, comparing their results to more traditional sampling methods. He’s highly optimistic about what it could mean for conservation science. “Environmental DNA is one of these unprecedented fields of science that everyone is interested in pursuing,” says Bajno. “I think there is no ceiling.”

“We’re slowly starting to develop that relationship, and trying to figure out the appropriate training tools to try to hand over some of that work.” Robert Bajno, DFO biologist

His excitement is warranted. Data collection would be made cheaper, which would allow much more information to be gathered. And eDNA would be particularly useful in the North. “The Arctic especially is huge, and there’s not a lot of people that live across the whole geographic area,” says Karen Dunmall, a DFO researcher who studies salmon in northern rivers. “Getting information about such a wide geographic space, about specific species, is difficult and takes a lot of time and money.”

Sending resource officers to remote parts of the country is expensive and logistically challenging, meaning scant data is collected for some of Canada’s most sensitive and rapidly changing regions. But with just a small amount of training, community members who are already out on the land—hunters, fishers, trappers, Canadian Rangers—can collect water samples that might provide even more information than a scientist on the ground.

Dunmall is already putting eDNA technology to work in the North. The salmon she studies are appearing in greater numbers and wider variety in communities up the Mackenzie River than they have in living memory or according to traditional knowledge. New colonizing species tend to be rare at first, so Dunmall says any tool that can lead to a quicker—and fuller—picture of the salmon influx is “an excellent step forward.” And that’s not just for researchers, but for Northerners who want to know more about what’s happening in their backyards and how changes might affect important subsistence, commercial or culturally valuable species.

Dunmall has partnered with communities in the Sahtu and Gwich’in regions. That’s how she met Freddie Furlong, a soft-spoken, 28 year-old trapper and fisherman from Aklavik.

Once or twice a day, Furlong sets out with cigarettes and a can of pop in his 18-foot aluminum SeaArk, motoring five kilometres up the Peel Chanel from his home to his fishing net. Before he pulls his net—often containing an assemblage of whitefish, coney, herring, jackfish, Arctic char, and salmon—he carefully takes water samples around it. The eDNA in the water upriver and downriver from his net is then checked against the fish he caught that day, to help fine-tune the nascent science. Finding the same fish in the net as in the eDNA downriver is a good sign, but Bajno says the eDNA sample will often find traces of additional fish that were not caught in the net.

“We’re slowly starting to develop that relationship, and trying to figure out the appropriate training tools to try to hand over some of that work,” says Bajno. “It’s not necessary for us to go up and sample ourselves when you have people that are very capable of doing it. They understand the environment, the ecology, the resource, the target organism much better than some of us.”


Peter Van Buren leans over the side of a large inflatable launch in Coronation Gulf, which separates Victoria Island from the mainland. He dips a plastic jug into the water and then empties it. Like Furlong at his fish net, he fills it again and empties it. After five rinses, Van Buren fills the jug once more and then pours its seawater contents into a fresh plastic bag and places it in a cooler until it can be frozen in a specialized -80C freezer. Three more of these bags and it will be off to the next collection site.

Scientists repeated this ritual—the rinsing, the filling, the cooler, the freezer—throughout the Canada C3 icebreaker’s 150-day voyage from Toronto to Victoria via the Northwest Passage last year. The aging MV Polar Prince served as mobile laboratory, collection platform, and a mothership for the launches that took scientists further afield to gather samples in one of the biggest eDNA surveys ever undertaken.

The main idea was to develop a broad baseline of species diversity across all three oceans and some freshwater systems, explains Kristi Miller-Saunders, a Fisheries and Oceans scientist who led the environmental DNA program for the Canada C3 expedition. That baseline is becoming more relevant than ever with the onset of climate change. Species like orcas, capelin and even beavers are migrating deeper into the warming Arctic. Meanwhile, entirely alien species deposited there by an increase in ship traffic are setting up shop and threatening to destabilize the ecosystem.

Only one invasive species, a red alga, is known to have permanently established itself in the Canadian Arctic thus far. But a study released in February 2018 found evidence of at least eight more, including species of barnacles, skeleton shrimp, snails, crabs and more, with a good chance of getting a foothold and persisting.

Species that evolved in the Arctic are being squeezed, not just by the changing habitat, but potentially also by competition, parasitism and predation from the newcomers. For Northerners, that could affect everything from fisheries and traditional hunts to fouling of engines and boat hulls. Cataloguing what belongs there and what doesn’t is long overdue. “It’s possible that there are incursions already in the Arctic of more southerly species,” says Miller-Saunders. But in the huge and chronically understudied Arctic, knowing the existence and extent of these incursions is difficult.

eDNA can not only help us get a sense of ecosystems today, but it can also be a window into the past. Since all that’s needed is water, a frozen sample from even a decade ago could be used to compare with contemporary findings.


Kristi Miller-Saunders’s office at the Department of Fisheries and Oceans in Nanaimo, B.C. overlooks Departure Bay, which, on a grey January afternoon takes on all the charming hue and tone of a concrete floor. Yet the adjacent bay is teeming with life. At any time there can be Pacific white-sided dolphins, orcas, humpback whales, sea lions and multiple species of salmon and herring. Everything in that water is shedding tiny clues of its presence.

Down the hall from her office is a lab humming with the machines that allow her to look at those clues. The process is similar to other DNA techniques, in that it involves replicating strands of DNA in specialized machines, then analyzing the strands for markers that indicate what species were in the sample. That basic technology, polymerase chain reaction, has been around since the 1980s—and won the 1993 Nobel Prize in Chemistry. Collecting DNA from the environment, similarly, has been around for a decade, but now the technique is being deployed at an unprecedented scale.

“Managing fisheries is hard,” celebrated British Earth system scientist and fellow of the Royal Society John Shepherd once told an audience at Princeton University. “It’s like managing a forest, in which the trees are invisible and keep moving around.” Environmental DNA is a way of counting—or at least accounting for—the fish without ever seeing them. Sure, it doesn’t give a precise count of how many of an animal are there, but using relative abundances of DNA, researchers are able to roughly estimate numbers—and the precision with which researchers can come to these conclusions is improving all the time. It’s especially useful for creatures that are hard to find, because it doesn’t care about colour, sneakiness, nocturnal habits or skittishness.

The delta, facing the Beaufort Sea, is experiencing dramatic changes.

Managers in Nahanni National Park are using eDNA to keep an eye on bull trout—an ideal species for that technology because it can occur in low densities across different habitats. “Environmental DNA techniques allow [managers] to identify species that they thought might not have been there because they’re so hard to find, or in such low abundance, that they’ve never seen them there before,” says Bajno.

Scientists and officials from Fisheries and Oceans departments across the country met in March to come up with a national vision for eDNA. Researchers were encouraged to explain to their managers just how vital this new piece of technology is. It was, according to Miller-Saunders, a rare instance where everyone was equally excited about “how to move forward in a big way” with the new tool.

In Aklavik, Furlong doesn’t profess to be collecting samples with a mind to push the boundaries of science. But knowing what the fish are doing would be useful to him and to his community, situated as it is in the Mackenzie Delta.

The delta, facing the Beaufort Sea, is experiencing dramatic changes. Not only is it sensitive to what happens upriver, as water drains from the second-largest drainage basin in North America, but it also faces the wrath of storms on rising seas, increasingly unimpeded by sea ice. It’s a perfect storm for perfect storms, like the once-in-a-thousand year event that hit in 1999, when briny Arctic seawater surged up the delta, drowning plants and saturating the marshes in salt with effects that linger today.

The work Furlong does five kilometres up the river from his home is helping build out a picture of the changes happening there. And while he does it, he’s helping scientists in Winnipeg and Nanaimo figure out how to deputize people like him to fill in the gaps all across the North.

It’s not outside the realm of possibility that every major river in Canada, every coastline with a furtive new species, could soon have an eDNA collection program monitoring the animals that live in and around them. As those tiny bits of information churning through the water are pieced together, all the distant, dimly understood corners of the country could become as clear as the waters they hold.