UMaine center amplifies the power of environmental genetics

by Erin Miller

Life in nature is notoriously difficult to track. Endangered species are inherently rare, and invasive species often show up in unexpected places. Animals who occupy our environment in abundance are often wary of humans or frequent places that are difficult to access, like the bottom of lakes or remote corners of the Maine woods. Once found, plants, animals or microbes are often difficult to identify without expert training.

Understanding where organisms are is a crucial first step to targeting conservation efforts, monitoring for invasive species, understanding the impact of climate change and reducing negative effects on people. For decades, researchers and conservationists used methods that required capturing or spotting a given animal, plant or microbe to determine if it occupied an area. These approaches can be time- and resource-intensive, particularly with rare organisms. 

The burgeoning field of environmental genetics uses technology like environmental DNA, or eDNA, to help scientists, agencies, conservation groups and others to track where organisms are with unprecedented scale, and often less cost. With a vial of water, air, soil or sediment, scientists can tease genetic samples from the cells species shed as they live and die in their environments. The approach also avoids contact with the organisms, reducing the need for highly-trained personnel, specialized sampling gear, collection permits and disturbance of sensitive species. 

“How often do we come up with something where it opens the door to the public to not just understand some aspects of the science, or the problems or challenges, but it brings them right in now to help work towards the solutions?” says Michael Kinnison, professor of evolutionary applications and director of the Maine Center for Genetics and the Environment (MCGE) at the University of Maine. 

MCGE seeks to develop resources and foster the adaptation of genetic technologies for the betterment of Maine’s environment. The center continually seeks collaborators across UMaine and from other research institutions who are interested in using environmental genetics in their research, as well as people or organizations who want to use environmental DNA to find out what lives in their backyards. 

The center is a spinoff of the Maine Environmental DNA initiative (Maine-eDNA), a five-year project supported by a $20 million grant from the National Science Foundation (Award #OIA-1849227) through the Maine EPSCoR program that aims to revolutionize environmental monitoring, ecological understanding and sustainability of coastal ecosystems. 

The resources developed at UMaine to power research for Maine-eDNA and MCGE also deliver services to Canadian tribes and people’s councils, state agencies from Maine and Massachusetts, and other tribes, universities, businesses, nonprofits and lake associations throughout New England. UMaine’s eDNA Laboratory, which is managed by Geneva York under the University’s Coordinated Operating Research Entities and supported by the Office of the Vice President for Research and Dean of the Graduate School, processed samples for more than 46 clients last year. 

“If you look at the uptick of who is eDNA now, you have certainly got the big agencies but you also see groups like the Native Fish Coalition, Trout Unlimited lake associations and tribes using eDNA as a part of their monitoring,” Kinnison says. “This helps them manage their lands and helps those groups reengage with their lands. They get out on the water, and collect the samples themselves, in many cases.”

The powerful tools have also caught the attention of researchers who are not geneticists. UMaine medical entomologist Allison Gardner joined the center to incorporate environmental genetics in her efforts to monitor for disease-toting mosquitoes. Chaofan Chen, a Maine-eDNA new faculty hire and assistant professor of computer science and cooperating faculty member of MCGE, is helping Kinnison and others use artificial intelligence to quickly and accurately process the vast amounts of data generated by sequencing genes from the environment. Darren Ranco, associate professor of anthropology and chair of Native American Programs at UMaine, joined MCGE help shape responsible approaches to environmental genetics that account for the right to data sovereignty, particularly for Maine’s tribal nations. 

Agencies like Maine’s Department of Marine Resources (DMR) are taking notice too. A study led by Vaughn Holmes, who conducted the work as an ecology and environmental sciences master’s student in Kinnison’s lab, demonstrated that eDNA detected the presence of searun rainbow smelt with greater accuracy, efficiency, safety and less cost. In response, DMR started using eDNA and the UMaine-led team’s tactics for employing it to survey several searun smelt streams in 2023. 

The tools promoted through MCGE are also powering species distribution mapping at unprecedented scales in Maine. Cody Dillingham, a wildlife ecology master’s student in the lab of UMaine fisheries scientist Joseph Zydlewski, single-handedly documented the range of sea lampreys and American eels in the Penobscot River watershed over a single field season. Without environmental DNA (eDNA) technology, the effort would have required a team of technicians combing the river and its tributaries over multiple seasons. Dillingham’s survey showed that sea lampreys and American eels are widely distributed in the Penobscot River basin and have recolonized large portions of their historic ranges following dam removals and fish passage improvements throughout the system.

The center and eDNA project also created hands-on research opportunities for undergraduate students like Lucia Liet, an ecology and environmental sciences major. In the lab of Erin Grey, another Maine-eDNA new faculty hire and assistant professor of aquatic genetics at UMaine, Liet used eDNA techniques to identify where Atlantic cod spawn in the Gulf of Maine. The fish has been functionally extinct for more than a century and, even with protective regulations, has not recovered like other over-harvested species. One theory regarding their meager recovery is that something going wrong with their spawning. 

“We don’t really know where they spawn,” Grey says. “We know a couple of areas, but it’s a big gulf and they spawn near the bottom. Since it can be easier to collect eDNA from water samples it might be easier for us to detect it.”

Students at Maine’s K-12 schools have learned more about their world thanks to MCGE resources as well. Beth Campbell, education, outreach and diversity project manager at Maine EPSCoR, piloted a project that helped kids advance environmental genetics research. Students collected samples that were processed by UMaine’s eDNA Laboratory which, in turn, shared the results with the young community scientists to facilitate further eDNA discussions in their classroom. 

As more people learn more about the potential of life’s detritus to map, quantify and study organisms and their habitats, Kinnison and his colleagues at MCGE hope that curious members of the public will reach out with their ideas. 

“We want people to let us know what they are thinking. We can often discern pretty quickly whether something’s realistic or feasible and give those people ideas about how to use environmental genetics,” Kinnison says. “We’ve got a lot of backyards in Maine. We can change what we know about the state with people from all walks of life starting to participate. ”

Contact: Erin Miller,