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GEN-FISH harnesses environmental DNA to manage Canada’s freshwater fish

April 7, 2020

Canada is home to almost 200 species of freshwater fish spread out over more than two million lakes covering about 7.6 per cent of Canada’s nearly 10 million square kilometres. Margaret Docker and her colleagues want to catalogue them all (the fish, that is).

“We are certainly not the only ones doing this, but we are likely the first ones doing it on this scale,” she said.

Docker is a fish biologist at the University of Manitoba with particular interest in lampreys and salmonids. It is this and her expertise in environmental DNA (eDNA) that she brings to the table as the co-lead of a 25-member team comprising the Genomic Network for Fish Identification, Stress and Health (GEN-FISH). Genome Canada is providing $4 million to the $9.1 million, four-year project, with the balance coming through Ontario Genomics, Genome Québec, plus university and industry partners.

Co-led by Daniel Heath from the University of Windsor and Steven Cooke from Carleton University, GEN-FISH aims to produce accurate, easy-to-use toolkits that can determine which fish species are present in a given water body and to estimate how many fish are there. This includes commercial species such as walleye (pickerel), trout, pike, perch, and bass; species at risk such as lake sturgeon and American eel; and invasive species such as sea lamprey in the Great Lakes.

“What I see as being really key is making sure it’s not just a research project, but that there are tools that will be available to all Canadians, particularly Canadian fisheries managers, by the end of the four years,” Docker said.

As its name implies, the eDNA approach involves taking samples from the environment such as bodies of water and then testing them for the traces of DNA that living things naturally shed into their environment. Genetic material, or markers, that are unique to a species need to be identified.

The GEN-FISH team plans to spend the next four years identifying these markers from fish species across Canada so they can be incorporated into DNA microarrays, also called “gene chips.” These devices, about the size of a postage stamp, contain microscopic samples of DNA that react when specific DNA markers are present.

GEN-FISH had its first team meeting in December 2019 and was well underway as of March 2020, but as with many research projects across the country, it is facing confounding factors from the COVID-19 pandemic.

“We’re just nicely getting going in our first field season and things have been put into a bit of disarray,” Docker said. “But we’re starting. We’ve broken into various working groups, a number of students have been recruited, and we’re hoping our first field season won’t be compromised too much. It’s coming together.”

eDNA offers a way to gather information that’s difficult to otherwise obtain. Traditional study methods such as netting are time consuming, expensive, and limited. They must be tailored for individual species (such as using different mesh sizes) and require crews with specialized training.

eDNA can scan for multiple species within a single water sample, detecting fish that other methods could easily miss. For example, some fish are known as “cryptic” or “secretive,” that is, their behaviours make them hard to detect with traditional study methods. 

“An example might be larval lampreys which spend most of their lives burrowed in the sediment in rivers and streams, so you wouldn’t see them easily,” Docker said. Nocturnal species might also get missed if sampling is done only during the day.

“It’s just a way of trying to get a better picture of what’s out there.”

GEN-FISH researchers will also gather data on how the DNA markers perform in the field. It’s critical that the technology in the GEN-FISH toolkits be thoroughly validated so users can be sure of their results.

For example, if the eDNA toolkit is being used to detect invasive species, users have to be confident it isn’t yielding “false positives,” that is, saying a species is there when it’s not.

“Management actions to deal with invasive species can be extremely costly, so we have to be sure that the test isn’t cross-reacting with a native species or picking up traces of contamination,” Docker said. “The beauty of eDNA is that it’s extremely sensitive and able to detect even rare species, but that also makes it vulnerable to contamination if sufficient controls are not in place. We want to make sure that the tests are all fully validated so that fisheries managers trust the results.”

Validating the GEN-FISH tests will be challenging. Results can be influenced by numerous different factors, from where in a water body a sample is collected, to the abundance of a particular species. In cold water, fish tend to shed less DNA, while in warmer waters, DNA degrades more quickly. For rare species, it might take testing several water samples to get a signal, while for plentiful species, the signal might be lessened if the water is moving.

The broad range of expertise on GEN-FISH is aimed at this aspect. For example, Mark Shrimpton from the University of Northern British Columbia is working on a project with Trevor Davies from the British Columbia Ministry of Forests, Lands, Natural Resource to essentially count every salmon that comes up and down a river on Vancouver Island over a period of three months.

“They’re willing to collect water samples for us every day for three months from this river, so we’re able to look at eDNA signal as fish are coming in and going out,” Docker said.

She explains this type of wide-ranging, cross-Canada work is where public research such as that funded by Genome Canada can really shine. The GEN-FISH toolkits will be easy to use and relatively inexpensive to manufacture. They will be useful to a wide range of users, from government fisheries managers to environmental consulting companies doing biodiversity assessments for industrial, commercial, or public works projects.

“It’s the sort of thing that consulting companies wouldn’t have the opportunity to develop themselves, but if they were available, they could then be used.”

The kits will also be useful at the community level, a fact that hasn’t escaped the GEN-FISH team. Some Indigenous communities have been engaged, and the researchers hope to expand this facet of the project.

“This seems to be something that would lend itself very well to some of these community monitoring programs,” Docker said.