Biological sciences faculty member Nicholas Sard is engaged in several grant-supported projects related to helping support the Great Lakes ecosystem.

A self-described fisheries geneticist –- a term for somebody who uses environmental DNA (eDNA) and other genetic techniques for the benefit of fish and other species –- Sard’s work includes playing a key role in two projects funded by the Nature Conservancy. Both projects involve collecting and filtering one-liter water samples to extract free-floating DNA and cells, collectively considered eDNA sampling.

Last year, Sard worked with The Nature Conservancy on a project called “Rapid survey for native and invasive Great Lakes fishes using environmental DNA methods.” The project was a success in that two new assays were developed and several native species were detected. As an expansion from previous work, Sard’s project with the Nature Conservancy this year was a “Survey of native and invasive aquatic species in rivers spanning SLELO and Adirondack PRISM programs.” The project worked with the St. Lawrence – Eastern Lake Ontario Partnership For Regional Invasive Species Management (SLELO PRISM) to search for invasive species in 14 waterways in the Eastern Lake Ontario Basin. 

Essentially the work, which included SUNY Oswego students, involves collecting and testing for the presence of DNA from invasive plants and animals in water samples, Sard said. In addition to finding invasive species, Sard, and a research student, John-Kaarli Rentof, are working to detect a threatened fish species -- the round whitefish.

“We’re sampling the community that resides in that watershed,” which can mean not just animals but also plants and creatures that are not water dwellers but might use tributaries and the body of water where the sampling takes place, Sard said.

The sampling can either be a species-specific assay –- asking “is DNA from my target species present?” –- or a general site survey, or asking “what’s here?,” Sard noted.

“The general idea is the earlier you can detect a new invasive species in an environment, the quicker you can eliminate this threat from that environment,” Sard explained.

Catching a killer

Some work focuses on the sea lamprey, which would sit atop the “least wanted” list, Sard noted, as the Great Lakes Fisheries Commission spends around $10 million per year trying to control the invasive species.

“They are parasites and they suck blood from fish, as part of their life cycle” Sard said. “It took them about a hundred of years to get established in a critical mass but once they did, you saw a population crash of lake trout and coregonines like cisco.”

But limits exist to sampling that requires researchers to try advanced genomic methods to improve efficacy, Sard said.

“Lake Erie has hundreds of tributaries, and researchers try to eliminate these invasive species when they find them in a process that is about 85 to 90 percent effective,” Sard said. “It’s roughly successful but there are so many sites and sources where they can come from. We find ourselves asking: Are they developing resistance or are they coming from unmonitored streams?”

Thus part of the project includes creating a RAPTURE (restriction site associated DNA capture) Panel, which can determine natal origins, or where sea lampreys are born and who they are related to.

“We have thousands of tissue samples procured per year, but the question becomes how many samples of adults and juveniles would you need?” Sard said. “Given past work, we probably can infer natal origins and differentiate between tributaries if you have a lot of data and sampling, but the question is, after accounting for imperfect data, can we still make meaningful inferences?”

Sard and two research students sought to better understand the above uncertainties using simulations. Their research involved running large, forward-simulations that involve tracking hundreds of thousands of fish across hundreds of places in their genomes across each animal’s life cycle for 20 simulated years. “The real challenge is in trying to reconstruct a pedigree without any parents at a Great-Lake-wide scale,” Sard said.

Sard analogizes it to investigators capturing a criminal using DNA evidence, and titled his past Science Today lecture on it “Catching a Great Lakes Killer.” 

“That’s what we’re trying to do,” he explained.

Studying sturgeon

In addition, Sard is involved in a project called “Contributions of sturgeon passage to annual lake sturgeon recruitment in the Upper Menominee River,” a sub-award contract from University of Wisconsin - Green Bay via the U.S. Fish and Wildlife Service. 

Researchers are supplementing sturgeon above the Menominee Dam in Wisconsin, which is “a real feat,” Sard said. “Sturgeon don’t like fish ladders. They prefer elevators.”

Thus the project involves transportation of sturgeon into this habitat. “My role is the pedigree reconstruction, or looking at how much the fish we’re moving up there contribute to the quantity of the offspring,” Sard said. 

Sard also works with a team from Cornell university on a project called “Molecular sexing of shortnose sturgeon to determine the feasibility of PCR-based methodology on higher ploidy sturgeon species,” funded by the Department of Environmental Conservation.

In 2020, a group in Europe found a locus –- a split in the genome –- to differentiate sex in sturgeons. Sard’s role was part of a wider effort to test a similar process among different species. His project focused on the shortnose sturgeon, which is listed as a endangered species in New York state. 

Implications for being able to infer sex include studying sex-specific migratory behaviors, as well as ratios of potential breeding partners because the difference in survival rates between the sexes can affect population growth and genetic diversity.

The research also has commercial implications in that a region’s caviar market as only females are used.

Overall, these projects contribute not only to improvements in the Great Lakes ecosystem but opportunities for Sard to teach and provide important research experiences for future generations of researchers.