Atlantic Canada’s freshwater fish capture N.B. ecogenomics expert’s attention

In the face of climate change and other pressures, Dr. Scott Pavey, a rising star in the new and promising field of ecogenomics, is focused on retaining the biodiversity of New Brunswick’s and Atlantic Canada’s freshwater fish and the industries that rely on them.

He runs what he proudly calls, “the most advanced ecology-focused genomics lab in New Brunswick.”

CRI Genomics, Dr. Pavey’s lab at the Canadian Rivers Institute, University of New Brunswick, Saint John, is known for applying state-of-the-art genomic technologies and techniques to investigations into how to conserve and manage freshwater fish stocks and make aquaculture and the fisheries that depend on them more sustainable.

This is important work, he said, because “All industries that alter the environment, such as mining and forestry, or discharge into the environment, such as pulp mills etc., have a responsibility to ensure their impacts do not adversely affect the habitat and populations of freshwater fish. Freshwater fish habitat is protected by federal legislation. Every EIS [environmental impact statement] for projects near freshwater must take freshwater fish into account.”

Reduced biodiversity, he said, “weakens the entire system because species exist in food webs and are reliant on each other. If the prey go extinct, the predator starves.” Dr. Pavey pointed out, freshwater has been heavily impacted in Canada and worldwide and when these impacts cause local extinctions of species; they reduce biodiversity.

Dr. Scott Pavey

Credit: Photo, Rob Blanchard, UNB Communications

Dr. Scott Pavey with CRI Genomics lab manager Larissa Roehl.

Credit: Photo, Rob Blanchard, UNB Communications

The lab of The Tier 2 Canada Research Chair in Aquatic Molecular Ecology and Ecological Genomics specializes in aquatic molecular ecology and ecological genomics. Aquatic Molecular Ecology uses molecular genetic tools for advanced DNA analysis, such as entire genome scanning and bioinformatics to identify and study communities of interdependent organisms in aquatic ecosystems. Ecological Genomics seeks to understand the genetic mechanisms that govern the way organisms respond to their natural environment. Ecology, evolution and conservation are Dr. Pavey’s watchwords.


Since 2020, he has been active in a $9.1 million Genome Canada Large-Scale Applied Research Project (LSARP) called GEN-FISH, short for Genomic Network for Fish Identification Stress and Health. It has involved a group of researchers, professionals and community members in an extensive and innovative four-year undertaking to develop toolkits that pinpoint where Canada’s more than 200 freshwater fish species can be found and in what numbers.

Accurate information on the kinds of fish and their numbers in rivers and lakes, he said means improved environmental monitoring, assessments and fish management. He explained, “Fish are under water, thus hard to see directly. It takes a huge effort to set nets. So, when there are impacts, they are often invisible. With eDNA we can more easily detect such impacts and recoveries

Also on the agenda are plans to develop a method to chart how Canada’s freshwater species are faring under increasing, mostly human-induced, stress. Project partners from Atlantic Canada include the New Brunswick Energy and Resource Department (NB ERD) and the Nova Scotia Salmon Association.

Dr. Pavey’s role is to extend the Ontario-based, but Canada-wide research to Atlantic Canada.


The project aims to produce three sophisticated toolkits, one for fish surveillance, another for fish health and a third for decision making that essentially promotes the other two toolkits for widespread general use.

“We are helping with developing, lab testing, and field testing the Fish Survey Toolkit,” said Dr. Pavey. “Assays need to be separately developed for each species before they are put on the chip. My graduate students are doing this, focusing on fish important to Atlantic Canada. They are also collecting eDNA [environmental DNA] samples in the field that we are using to field validate our developed tools.”

The fish in this region, he said, “are important because they are in Atlantic Canada. They also have commercial fishing, recreational fishing and cultural importance.”

Dr. Pavey said, “Our lab is going to submit sequences for the first draft Fish Survey Toolkit in a month or so. We are focusing on 15 species important to Atlantic Canada. We expect to have several draft toolkits in year three of the grant and test them in real conditions, including rivers and lakes in New Brunswick. We will have finished products in two years.“

Interest in these products is expected to be strong, especially from the fish management and environmental sectors and from some industries too. Many of them have a need to monitor their environmental impacts on freshwater from such things as industrial effluent. “Current entities requesting my services include the federal and provincial governments, non-profits, first nations and private consulting,” he said.

The Fish Survey Toolkit, he said, will let users know whether any of the Canadian fish species included for identification on the toolkit chip is present in any particular lake or river, based on analyses of water samples collected from them.

For this project, Dr. Pavey’s lab has been working on identifying fish species from environmental DNA. He explained the process this way: “A water sample is taken from a waterbody. The water is filtered and cells from fish that were in that waterbody collect on the filter. We prepare the DNA so that we can use a chemical reaction to make copies of the segment of DNA that is unique to a single species. If the species’ specific reaction produces a product, we know that species was in the water body.”

Fish-Health Toolkit

“The Fish Health Toolkit,” he said, “is designed to answer what is causing fish to be sick or die. Is it high temperatures? Heavy metal toxicity? Etc. The latter would involve lethal sampling of the individuals in question and determining which ‘stress’ genes are turned on or upregulated to tell us the nature of the ailment.”

Dr. Pavey is certain the toolkits will bring more attention to conserving and sustaining the Atlantic region’s freshwater resources. “They absolutely will,” he said. “They will be a new tool that will allow high throughput testing.” That means high volume testing with quick results.

“We have partnered with DFO [Department of Fisheries and Oceans] and NB ERD and both organizations are very excited to use these tools. Because I’m involved with the grant, I will ensure that the tools are designed in a way it meets the needs of organizations in Atlantic Canada.”

Considering Canada has one-fifth of the earth’s freshwater resources, the need for these toolkits quickly becomes apparent.

Meanwhile the GEN-FISH project has sparked new ideas for exploration. “While GEN-FISH is primarily focused on presence/absence of species, we are experimenting with how to use similar techniques to estimate abundance,” he said.

Other Work at CRI Genomics

In other work at CRI Genomics, Dr. Pavey noted “the lab team has spent a lot of time focusing on fish such as Atlantic Cod, and looking at factors that could help their populations rebound.” Striped Bass, Bluefin Tuna and the American Eel are other species to which his team has given special attention. All these fish species are of concern under the Canadian Species at Risk Act. His team used DNA sampling from tissue to determine population interactions and environmental adaptations of these species.

His recent research on the American Eel with Dr. Louis Bernatchez at Laval University identified the genes responsible for the eels’ survival in freshwater and saltwater environments. Genetic analysis of the all-female eels in the Upper St. Lawrence River, showed they had unique adaptive genetic traits compared to counterparts reared in brackish or saltwater.

It was an important finding because that kind of knowledge can result in more nuanced fisheries management policies to protect habitat and migration routes of sub populations that need critical genetic consideration.

The considerable range of CRI Genomics’ capabilities, means Dr. Pavey’s eight-member team is kept busy, often by clients seeking customized services unavailable elsewhere in the region. The client list includes the NB Museum, Huntsman Marine Science Centre, Memorial University, the Department of Fisheries and Oceans, the University of Massachusetts and NovaEel, a Nova Scotia-based aquaculture start-up.

The lab can do genotype-by-sequencing, also known as GBS, to enable researchers to track down the genetic roots of observable traits such as size or colour in fish, for instance. It can also identify unique adaptations found in local fish species, employ sequence barcode regions in DNA to identify species in microbiomes or insect communities, and use the environmental DNA found in small tissues and cells suspended in the waters of lakes and rivers to identify species that inhabit them. In addition, the lab has the capacity to run simultaneous targeted resequencing of candidate genes from many individuals.

With these resources, Dr. Pavey has set himself an important agenda in preserving the biodiversity of Atlantic Canada’s freshwater fish.

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