• Sydeny Currier, a graduate student from the University of Windsor, uses a pipette while doing some genetic work on fish samples. (Photo: Naomi Pelki)

Understanding the behaviour and movement of fish in Canada has always been important, for both the fishing industry and for protecting species that are at risk.  

A new, harmless and economical way to study the diversity, movement and distribution of fish species in waterways has already led to some surprising findings in Canada and across the globe.

Environmental DNA research, also known as ‘eDNA’, involves testing water for genetic material from cells released by fish as they swim around. This kind of research is relatively new--with the technology to complete this kind of research being introduced about ten years ago. 

“One of things I’ve learned from doing environmental DNA work with fish is you are always surprised,” says Dr. Daniel Heath, a professor at the Great Lakes Institute for Environmental Research, Department of Integrative Biology. “The reason we think we understand what fish do is based on capturing them, but that is a very coarse way in determining what fish behaviour is.”

In the United States, migration patterns for some marine species appear to be shifting in the Atlantic Ocean, as genetic traces of some species have been found further north of their usual southern homes.

A study published in the journal Frontiers in Marine Science on May 5 highlights how the Brazilian cownose ray, for example, have been found in New Jersey’s Barnegat Inlet when the weather is warm. Previously, the ray had never before been recorded in the United States north of the Gulf of Mexico.

“A possibility is that they are likely moving north because the water is getting warmer,” says Mark Stoeckle, the lead researcher of the study. “It’s happening with animals on land, and it is happening with fish in the ocean.”

For a long time, scientists have understood fish migration patterns and behaviour by tossing in nets to catch the species or by electroshocking, among other methods. 

But eDNA has proven to be a “low-tech, harmless way to monitor changes in fish ranges,” Stoeckle says, adding that work is now underway to study the relationship between the concentration of species’ DNA in water and the abundance of that species.

“It is a revolutionary technology and I think this is going to really help us understand and better monitor and protect our oceans,” he says. “There is a growing community of researchers around the world who are applying these exact same techniques to the environments they are studying.”

Dr. Daniel Heath is the lead biologist for the GEN-FISH project — a four-year project involving 23 researchers. (Photo: Tory James)

In Canada, a new project called GEN-FISH, led by Heath, involves developing sensitive detection assays for the DNA of every fish in Canada. The University of Windsor was recently given a $9 million grant from Genome Canada to work on this project, which started in January 2020 but has since been sidelined due to the COVID-19 pandemic. The GEN-FISH program is funded by the Government of Canada through Genome Canada, as well as the Ontario Genomics Institute. 

“The people who make decisions on the laws about protecting species at risk need to believe this technology is fool-proof,” Heath says. “We’re going to do this to a high set of standards to make sure that if you get a detection of a particular species of fish, that you know it wasn’t just a mistake of the marker.”

The purpose of GEN-FISH is not only to protect species at risk by understanding where they are present in Canadian waters, but also to monitor the fish that are exploited for commercial purposes so they are not over-harvested. Tracking where fish species are present can also help re-introduce them to areas where they have been wiped out.

“When you start using a tool that is really sensitive, quick and easy, you get a lot more data and start discovering stuff you didn’t expect,” he says. “If you go into a river system you think you understand completely, and you use environmental DNA to find out what species are actually there, you will get surprises.”

For example, three years ago researchers discovered the invasive round goby in the Great Lakes travels further north than anyone had previously thought. 

“We believed that dams would stop round gobies, but apparently they don’t,” says Heath. “We didn’t know how they got so far north but once we realized they were moving up the rivers faster than we thought, people had to come up with better ways of trying to slow them down.” 

Research can also show predator qualities

Environmental DNA research is not just for studying the cells that are released off the slimy outer layer of a fish, Heath says. It can also be used to determine what was in the stomach of a predator fish, proven by recent findings about the behaviour of yellow perch in the Great Lakes. 

“What we found was yellow perch that are in Lake Eerie eat an awful lot of yellow perch . . . it was a huge surprise to us,” Heath says, adding that a single yellow perch can cannibalize up to 20 baby yellow perch. 

Scientists have previously documented that some fish species like yellow perch do cannibalize, he says, but it has always been assumed as an accidental process rather than a major factor in terms of mortality for the species.

“With the numbers we were calculating, it is showing to be more common than I had ever heard of,” Heath says.

There are no confirmed numbers or trends that can be officially reported right now as the study is set to be submitted for publication this summer. But since yellow perch is a major commercial harvested fish in Lake Eerie, Heath says fisheries managers are already excited about these findings.

Knowing the number of baby yellow perch that are eaten by their parents can change how people calculate the number of perch that are going to be produced for commercial harvest, he explains.  

“When fisheries managers are calculating how many fish are going to be produced every year that can be collected by commercial fisheries, they have never included cannibalism in those calculations,” he says. Thanks to eDNA, this could now change — and could explain why models aren’t always accurate. 

The hope, he says, is to develop accurate and reliable markers for all fish species in Canada in the next three years. Through data collected by eDNA, the plan is to develop all these markers so that they are also very easy to use. 

“It will be a game-changer for everyone who works in fish research or fish management and conservation,” Heath says. “We also want this tool to be easy enough to use so cottagers in northern Ontario, for example, can know what fish are in their lake.”

One thing is for certain, he says. Environmental DNA will surely uncover more surprises about Canada’s fish, from coast to coast