Matthew Yates on shores of lakeMatthew Yates plans to use environmental DNA to get a clearer picture of which fish live in the Great Lakes and what they eat.

Researcher using DNA to unlock the mystery of what is living in the Great Lakes

The Great Lakes are teeming with DNA and this genetic information could help with fish management and sustainability.

DNA that’s been sloughed off the surface of or excreted by organisms is called environmental DNA or eDNA and it floats around in bodies of water. Integrative biology post-doctoral fellow and researcher with the Great Lakes Institute for Environmental Research (GLIER) Matthew Yates plans to use this eDNA to paint a clearer picture of which fish are living in the Great Lakes and what they are eating.

“This extra-organismal DNA is found in the environment, in soil, air, and water — I work with fish and fish are covered in mucus and scales and they’re constantly defecating in the water and so all that has trace quantities of DNA,” says Dr. Yates.

“Molecular genetic analyses have advanced in the last decade to the point where just by filtering water we can analyze this trace amount of DNA to tell which species are in the lakes.”

In addition to eDNA, Yates will also analyze the stomach content DNA to determine what the freshwater fish predators eat.

“Visual gut content analysis can tell you what predators are eating but it is often degraded by stomach acids so with DNA analysis methods, we can accurately determine what species these top predators from the Great Lakes ecosystem are eating,” he says.

“We can apply these genetic tools and use stomach content DNA to determine what these fish are eating, then we can use eDNA from the same environment to determine what is present in environment — telling us what is even available in the environment to eat.”

By using a combination of eDNA and stomach content DNA sampled from the same area, Yates hopes to understand diet preferences and determine whether predator fish are eating what is available in this environment or if they selectively choose their prey targets.

Yates and his team will also be developing new molecular tools needed for DNA analysis in connection with Genomic Network for Fish Identification, Stress and Health (GEN-FISH).

“All of this has important implications for understanding the ecosystem dynamics in the Great Lakes and has important implications for key fisheries species: recreational, Indigenous, and commercial,” says Yates.

“For example, predator-prey interactions can affect how organisms respond to environmental changes, such as those caused by global warming. Predation by invasive fishes can also have really negative effect on species that are already of conservation concern.”

With funding from the Co-operative Institute for Great Lakes Research, Yates will receive co-mentorship from three scientists: Daniel Heath, UWindsor integrative biology professor and researcher with GLIER; Subba Rao Chaganti, an assistant research scientist with CIGLR; and research fishery biologist Edward Rutherford from the National Oceanic Atmospheric Administration Great Lakes Environmental Research Laboratory.

“The application of molecular genetic, or genomics, tools to Great Lakes fish management and conservation is a game-changer and may help us slow, or even reverse, the loss of freshwater biodiversity,” says Dr. Heath. “Dr. Yates is at the forefront of that work.”

Fish sampling will commence in summer 2022.