What is eDNA?
Environmental DNA, or eDNA, is genetic material that organisms leave behind in their natural surroundings. This can include skin cells, scales, mucus, feces, urine, reproductive material, and other biological material released by an organism. In aquatic environments, this genetic material can become suspended in the water and move with the flow of a river, stream, or other waterbody.
The amount of time eDNA remains detectable in the environment can vary depending on several factors, including temperature, sunlight and ultraviolet radiation, microbial activity, water movement, and the natural breakdown of biological material. Because eDNA does not remain in the environment indefinitely, detecting DNA from a species can provide evidence that the species has recently been present in or connected to the sampled waterway.
One of the biggest advantages of eDNA is that it allows scientists to look for species without having to catch or see them directly. This can be especially useful when an invasive species are present in low numbers, difficult to find and survey for, or are located in a large waterbody. By adding eDNA sampling to traditional field surveys, CRISP can cover a broader area and look for invasive species earlier.
How Does eDNA Sampling Work?
The Catskill Center's CRISP program operates both terrestrial and aquatic invasive species teams. Currently, eDNA sampling is being conducted by the Aquatic Invasive Species Strike Team using a specialized eDNA sampling backpack.
Aquatic environments are particularly well suited for eDNA sampling because genetic material can be transported through the water. In rivers and streams, water movement carries biological material downstream, allowing sampling to provide information about species that may be present within a connected waterway. Lakes and other waterbodies can also be sampled at selected locations to monitor areas where invasive species may be present or spreading.
During sampling, water is passed through a fine filter that captures suspended biological material. The filter is then preserved and shipped to a laboratory where the collected DNA can be analyzed for species of interest.
eDNA sampling is more difficult in terrestrial environments. Genetic material is not distributed as evenly through soil as it can be through water, and soil can contain substances that interfere with genetic testing. These factors make it more difficult to collect representative samples and consistently detect target species in terrestrial environments.
(pic of eDNA sampling backpack)
Chesapeake WILD Grant
In Feb 2026, the Catskill Center was awarded a $53,600 Chesapeake Watershed Investments in Landscape Defense (Chesapeake WILD) grant to support early detection of aquatic invasive species in the Upper Susquehanna Watershed through eDNA sampling. The grant is funded by the U.S. Fish and Wildlife Service in partnership with the National Fish and Wildlife Foundation.
With this funding, the Catskill Center will conduct early detection eDNA sampling to identify aquatic invasive species that may be establishing in local waterways. Where invasive species are detected, the project will follow up with traditional field sampling methods to assess population density and distribution and determine the most effective management and spread prevention strategies.
This work builds on CRISP's ongoing efforts to advance education, prevention, early detection, and control of invasive species throughout the Catskills. Early detection is especially important because taking action when an invasive species is first becoming established can be much more effective than trying to control a population after it has spread across a large area.
The goal of this project is to proactively protect the long-term health of New York State's waterways and native biodiversity. By allowing the Catskill Center to detect invasive species earlier and across broader stretches of streams, rivers, and lakes, eDNA can strengthen the region's ability to protect the native fish, amphibians, invertebrates, and plant communities that make up the Upper Susquehanna ecosystem.
Where Are We Sampling?
The Upper Susquehanna River is a major tributary of the Chesapeake Bay watershed. The waterways that flow into it connect a large network of streams, rivers, and lakes and can provide pathways for aquatic invasive species to spread. Sampling multiple locations helps CRISP identify areas where invasive species may be present and where additional monitoring or management may be needed.
CRISP's eDNA sampling is focused primarily on waterways in the western region of the Catskill Park and surrounding areas that flow into the Upper Susquehanna River. Sampling across these connected waterways allows the Catskill Center to monitor a larger area and better understand where high-priority invasive species may be present.
Sampling locations include:
Charlotte Creek, Otsego Lake, Canadarago Lake, Unadilla Lake, Unadilla River, Oaks Creek, Crumhorn Lake, Cherry Valley Creek, Butternut Creek, Chenango River, Tioughnioga River, Chemung River, among others.
(pic of map of eDNA sampling locations)
What Are We Looking For?
The eDNA project focuses on aquatic invasive species that are considered important management priorities for the region. CRISP currently works with approximately 53 invasive species of regional interest for monitoring and management.
The eDNA sampling equipment is not limited to detecting these 53 species. Rather, these are the species that CRISP is particularly interested in monitoring because of their potential impacts and relevance to the region. The laboratory analysis is designed to look for specific genetic markers associated with the target species included in the project.
(link to CRISP invasive species list)
What Is the Data Used For?
The main purpose of collecting eDNA data is early detection. Identifying an invasive species as early as possible gives managers more information about where it may be present and allows them to investigate before the population becomes more widespread.
By sampling many locations along rivers and lakes, CRISP can build a better picture of where high-priority invasive species may be present and track changes in their distribution over time. Repeated sampling can also help identify areas that may need additional monitoring or field surveys.
A positive eDNA result does not tell us exactly how many organisms are present or how large a population is. Instead, it provides evidence that DNA from a target species was detected in the sample. This result can then be followed up with traditional field sampling to determine whether the species is present, where it is located, how large the population may be, and what management response may be appropriate.
The data generated through this project will help inform invasive species management plans and guide decisions about where monitoring, control, and prevention efforts should be focused. It can also contribute to efforts to protect rare, threatened, and endangered species and the habitats they depend on.
Where Does the Data Go?
After sampling is completed, the filters containing the collected environmental material are carefully preserved and shipped to the Environmental DNA & Genomics Core Facility (EGCF) at Cornell University for analysis.
The Cornell facility specializes in environmental DNA and genomic analysis. Laboratory testing looks for genetic markers associated with the invasive species of interest. Methods such as quantitative PCR (qPCR) and digital droplet PCR (ddPCR) can be used to test samples for species specific DNA sequences. Multiple species can also be tested from the same sample using multiplex assays.
( link to Cornell Environmental DNA & Genomics Core Facility website)
Once the laboratory analysis is complete, the results provide CRISP with information about which target species were detected in each sample. This information can then be used to identify potential detections, prioritize follow-up field surveys, monitor changes in species distribution, and help guide invasive species management decisions.
Which invasive species are high priority?
