Environmental DNA (eDNA) Assay for Monitoring Recovery of River Herring

News | Raritan River Initiatives

Mid-Atlantic populations of river herring (Alosa pseudoharengus, alewife, and A. aestivalis, blueback herring) have declined precipitously in recent years. River herring are listed as “Species of Special Concern” by the National Marine Fisheries Service. With over 1,700 dams in New Jersey, barriers to spawning migration are significant impediments to restoring river herring populations. Over the past seven years, four major dams have been removed within the Raritan River watershed, aiming to improve fish passage and restore freshwater spawning habitat for river herring (the Calco dam in 2011; the Roberts Street dam in 2012; the Nevius Street dam in 2013; and an additional dam on the Millstone River in 2017). Given all this investment in dam removal, we must effectively evaluate the success of such efforts. Environmental DNA (eDNA) has recently emerged as a powerful tool for surveying rare fish species (Ficetola et al. 2008, Jerde et al. 2011), and is already being deployed in a variety of fisheries monitoring programs. The technique is ideally suited to document the presence/absence of endangered species within habitats where they are very rare.

Our primary goal was to develop eDNA assays for tracking the return of river herring into habitat newly opened via dam removal in the Raritan River watershed. We intended to develop and test eDNA assays that could distinguish between alewife and blueback herring, while also distinguishing between other co-occurring Alosine species (e.g., shad). Dr. Olaf Jensen and his research group collected field samples of river herring and Dr. Julie Lockwood and her research group performed all subsequent molecular eDNA design experiments.

Upon receiving DNA sequences of each river herring species, we evaluated the degree of genetic variation between species at various target DNA regions. We found there was insufficient consistent genetic variation at these regions to design eDNA assays capable of distinguishing between two river herring species.  Thus, we cannot design effective species-specific assays for monitoring the recovery of each river herring species.  However, we will adopt an existing eDNA assay that is capable of detecting, but not distinguishing, the two species and proceed to full deployment of an eDNA survey to assess the success of dam removal on recovering river herring populations in the Raritan.

Mini-grant funds were used to pay summer salary for a PhD student to perform all molecular analyses (DNA extractions, PCR and sequencing prep), as well as for lab kits and chemistry to perform DNA extractions, PCRs and cleaning and quantification of amplified DNA products for sequencing. Funds were also used to pay for Sanger sequencing of amplified PCR products.

The project team included Dr. Olaf Jensen, Associate Professor, Department of Marine & Coastal Sciences, Dr. Julie  Lockwood, Professor and Chair, Department of Ecology, Evolution and Natural Resources, and Kathleen Kyle, PhD Student.

For more information, contact julie.lockwood@rutgers.edu, 848-932-9336, lockwoodlab.com.  This work was supported by a 2019 Rutgers Raritan River Consortium Mini-grant.