Nicholas Sard, a member of the Faculty of Biological Sciences, is involved in several funded projects related to supporting the Great Lakes ecosystem.
A self-described fisheries geneticist — a term for someone who uses environmental DNA and other genetic techniques to benefit fish and other species — Sard’s work includes a key role in two Nature Conservancy-funded projects. . Both projects involve the collection and filtration of one-liter water samples to extract free-floating DNA and cells, collectively referred to as environmental DNA sampling (eDNA).
Last year, Sard worked with The Nature Conservancy on a project called “Rapid Survey of Great Lakes Native and Invasive Fish Using Environmental DNA Methods.” The project was a success as two new tests were developed and several native species were detected. Building on previous work, Sard’s project with the Nature Conservancy this year was a “survey of native and invasive aquatic species in rivers spanning the SLELO and Adirondack PRISM programs.” The project worked with the Partnership for Regional Invasive Species Management of the St. Lawrence and Eastern Lake Ontario (PRISME SLELO) to search for invasive species in 14 watercourses in the eastern basin of Lake Ontario. .
Essentially, the work, which included students from SUNY Oswego, 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 an endangered species of fish – the round whitefish.
“We are sampling the community that resides in this watershed”, which can mean not only animals but also plants and creatures that are not water dwellers but could use tributaries and the water body where the sampling takes place, Sard said.
Sampling can either be a species-specific test — asking “Is my target species’ DNA present?” — or a general survey of the site, or asking “what’s in here?” Sard noted.
“The general idea is that the sooner you can detect a new invasive species in an environment, the sooner you can remove that threat from that environment,” Sard explained.
catch a killer
Some work focuses on sea lamprey, which would top the “least wanted” list, Sard noted, because the Great Lakes Fishery Commission spends about $10 million a year trying to control invasive species.
“They are parasites and they suck the blood of fish, as part of their life cycle,” Sard said. “It took about a hundred years for them to settle into a critical mass, but once they did, you saw a population crash of lake trout and coregonines like the cisco.”
But there are limitations to sampling that require researchers to try advanced genomic methods to improve efficiency, Sard said.
“Lake Erie has hundreds of tributaries, and researchers try to remove these invasive species when they find them in a process that’s about 85 to 90 percent efficient,” Sard said. “It’s pretty much done, but there are so many sites and sources they can come from. We wonder: are they developing resistance or are they coming from unmonitored flows? »
Thus, part of the project includes the creation of a Restriction Site Associated DNA Capture (RAPTURE) panel, which can determine the natal origins, or birthplace of sea lampreys and to whom they are related.
“We have thousands of tissue samples obtained each year, but the question is how many adult and juvenile samples would you need?” said Sard. “Given previous work, we can probably infer natal origins and differentiate tributaries if you have lots of data and sampling, but the question is, after accounting for imperfect data, can we still make inferences meaningful?”
Sard and two student researchers sought to better understand the above uncertainties using simulations. Their research involved running large forward simulations that involve tracking hundreds of thousands of fish through hundreds of places in their genomes throughout each animal’s life cycle for 20 simulated years. “The real challenge is trying to reconstruct a pedigree without any Great Lakes-scale parents,” Sard said.
Sard draws an analogy to investigators capturing a criminal using DNA evidence and titled his previous Science Today talk about it “Catching a Great Lakes Killer.”
“That’s what we try to do,” he explained.
Study the sturgeon
Additionally, Sard is involved in a project titled “Contributions of Sturgeon Passage to Annual Lake Sturgeon Recruitment in the Upper Menominee River”, a subcontract from the University of Wisconsin – Green Bay through the US Fish and Wildlife Service.
Researchers are completing sturgeon above Menominee Dam in Wisconsin, which is “a real achievement,” Sard said. “Sturgeon don’t like fish ladders. They prefer elevators.
Thus, the project involves the transport of sturgeons in this habitat. “My role is to rebuild the pedigree, or see how much the fish we bring up there contribute to the amount of offspring,” Sard said.
Sard is also working with a team from Cornell University on a project entitled “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 larger effort to test a similar process among different species. His project focused on the Shortnose Sturgeon, which is listed as endangered in New York State.
Implications for being able to infer sex include the study of sex-specific migratory behaviors, as well as potential reproductive mate ratios, since the difference in survival rates between the sexes can affect population growth and genetic diversity.
The research also has commercial implications as one region’s caviar market uses only females.
Taken together, these projects not only contribute to the improvement of the Great Lakes ecosystem, but also provide SARD with the opportunity to teach and provide important research experiences for future generations of researchers.