Rapid Detection of Atlantic Salmon and Trout in the Boquet and Ausable Rivers Using Environmental DNA

Carrianne Pershyn; Liz Metzger Ausable River Association (2026). Rapid Detection of Atlantic Salmon and Trout in the Boquet and Ausable Rivers Using Environmental DNA. Technical Report #121, Grand Isle, VT. Lake Champlain Basin Program.

This project used environmental DNA to map the distribution of brook trout in the Ausable River Watershed and understand the distribution of introduced trout species in the same waters. The environmental DNA work gave a landscape level understanding of where trout live without capturing them. Genetic material from fish and other wildlife is released through bodily fluids and is free flowing in the aquatic environment for a brief period. The material can be captured by filtering stream water and processing the samples using quantitative polymerase chain reaction (qPCR) in a genetics lab to determine whether a particular fish was present or absent at the time of sampling. This cutting-edge technique gives  a snapshot in time of where fish are and is particularly useful for detecting rare species or species with small populations. Thanks to research like this in the western US, when genetic material is found at one site, one or more fish are present in the kilometer above that site. By sampling a stream at one-kilometer intervals, maps can be created of fish presence and absence across the web of streams that make up the watershed. This technical grant project awarded by Lake Champlain Basin Program in 2020, enabled Ausable River Association scientists to explore and document the spatial distribution of four different species of salmonid in the Ausable and Boquet River watersheds in New York State. Over a two year period, water was collected and filtered from a network of over 150 kilometers of river and stream and found DNA evidence of brook trout, brown trout, rainbow trout, and Atlantic salmon.