Genome project aims for better grip on health of Canada's freshwater fish

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There are many good reasons to get a better grip on how fish are faring in Canada’s two million lakes, not the least of which is that they can be eaten.

“There is a lot of fish in those lakes. It’s opportunity to tap a new food source to help meet global demands for sustenance,” says Western University biology professor Bryan Neff.

“It’s probably the biggest single untapped natural resource in the world.”

With a predicted “massive” global shortage of animal protein 20 years down the road, and farming already stretched and oceans over-fished, Canadian freshwater fish could become an important source of protein, Neff said.

Apart from the Great Lakes, any of Canada’s lakes are under-used, he said.

“When we think of freshwater fish, it pales in comparison to actual commercial fisheries,” Neff said. “We just don’t fish our lakes that much, so there’s this huge untapped resource.”

Neff is one of 10 principal investigators in the Gen-Fish project investigating the health of Canada’s freshwater fish by examining DNA scooped right out of lakes. The project began late last year.


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Almost two dozen researchers from schools, Indigenous groups and government agencies will join with the help of a $9.1-million grant from the non-profit Genome Canada for a multi-year research program to manage and conserve freshwater fish stocks. Other partners such as provinces and universities will provide other funding.

The team will use the DNA fish leave behind in the water, a kind of environmental DNA, to help get a better picture of whether or not Canada’s freshwater fish are flourishing. Environmental DNA, also known as eDNA, also can be extracted for other species from the soil and air.

“What we’re trying to do is further advance a technology that’s relatively new but is available today,” Neff said. “You can learn a lot about organisms from their DNA.”

Neff, whose love of fishing dates back to his childhood summers in Muskoka, said once the DNA sequence is determined, the fish species can be identified.

“That is quite exciting,” he said “We don’t have to capture the fish or necessarily have to see them, but we know DNA came from that species of fish. The important thing about this grant is we’re using Canada as our test bed.”

Their findings will help determine how best to manage the more than 200 freshwater fish species found in Canada, of which about one-quarter are considered at risk.

The eDNA could provide “an early warning system” for fish facing potential threats such as pollution and climate change.

“We don’t want our freshwater lakes to end up like the oceans,” Neff said.

“We’ll hopefully be able to find answers for not just what is in that lake, but how many (fish) and if they are changing in abundance.”

Fish, he said, are particularly susceptible to global warming because they can’t regulate their own body temperaure.

“I’m very passionate about finding out what is going to happen in 50 years when our lakes are all one or two degrees warmer in the summer,” Neff said. “Are our fish going to be OK? Sometimes the answers are going to be no.”

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