Environmental DNA Detection and Quantification: A New Test For Great Lakes Native and High-Risk Invasive Fish Species

Surveillance, control, and eradication of invasive species, as well as monitoring endangered fish species, are global conservation management concerns for which effective management often depends upon accurate species detection and population quantification at low abundances. At least 186 invasive species have become established in the Laurentian Great Lakes basin (of which 25 are fishes), causing an estimated $5.7 billion annually in damages and control costs. This research project is developing a next-generation sequencing test to accurately detect, identify, and quantify all established and potential high-risk invasive fish species (from NOAA’s Great Lakes Aquatic Nonindigenous Species Information System (GLANSIS) watchlist, the literature, and our laboratory's work on Ponto-Caspian gobies) in the Great Lakes using environmental DNA (eDNA) from ballast and water samples collected in the field. We developed primers to recover ~100 bp sequences containing single nucleotide polymorphisms (SNPs) informative for distinguishing among all invasive and native  fish species, for the cytochrome oxidase subunit I (COI) and cytochrome b (cyt-b) mitochondrial DNA genes and the RAG1 nuclear gene. We are ground-truthing our test results using eDNA isolated from water samples frozen in summer 2012 by the Ohio EPA, with their fish counts taken concurrently using electrofishing and netting. We also are testing aquaria water housing known species and abundances. Ultimately, this test is designed to: (1) improve the ability to quickly and accurately detect and quantify invasive species at low abundances to facilitate rapid response actions, (2) help stop the introduction of new invasive species through enhanced surveillance (e.g., ballast water), and (3) control and reduce the spread of invasive species already present in the ecosystem through up-to-date provision of critical management information.