Asian Carp detection

Indirect, non-invasive detection of rare aquatic macrofauna using aqueous environmental DNA (eDNA) is a relatively new approach to population and biodiversity monitoring. As such, the sensitivity of monitoring results to different methods of eDNA capture, extraction, and detection is being investigated in many ecosystems and species. One of the first and largest conservation programs with eDNA-based monitoring as a central instrument focuses on Asian bigheaded carp (Hypophthalmichthys spp.), an invasive fish spreading toward the Laurentian Great Lakes. 

Since 2010, detection of Asian Carp environmental DNA testing warns scientists, policymakers, and the public that these invaders are knocking on the Great Lakes' door. However, new research published by scientists of the University of Notre Dame shows that the tools currently used for Asian Carp eDNA monitoring often fail to detect the fish. By comparison, new eDNA methods described in this study capture and detect Asian Carp eDNA more effectively.

Using an experimental pond containing Asian Carp the researchers found that currently used methods detect speciess-specific eDNA less than 5% of the time. In contrast, their new methods detected Asian Carp eDNA 95% of the time. The new, more sensitive toolkit includes an updated DNA capture method and a new genetic test to both detect and quantify DNA. Due to the high mitochondrial DNA similarity between the two species Hypophthalmichthys nobilis and Hypophthalmichthys molitrix and their extensive hybridization in the some regions the researchers designed a genus-specific qPCR assay to exclusively measure the concentration of bigheaded carp eDNA in environmental samples. 

This quantification allowed them to demonstrate that the new method captured five times more Asian Carp eDNA than the current method. Since the new method is also 40 times cheaper, they recommend the new toolkit to replace old methods in ongoing efforts for early detection of Asian Carp in the Great Lakes region and beyond.

Our new, more sensitive assay provides a quantitative tool for eDNA-based monitoring of bigheaded carp, and the higher-yielding eDNA capture and extraction method we describe can be used for eDNA-based monitoring of any aquatic species.