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Updated: Aug 30, 2025

Development and Testing of Species-specific Quantitative PCR Assays for Environmental DNA Applications
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Integrating invasive species risk assessment into environmental DNA metabarcoding reference libraries.

Andrew R Mahon1, Erin K Grey2, Christopher L Jerde3

  • 1Department of Biology, Central Michigan University, Mount Pleasant, Michigan, USA.

Ecological Applications : a Publication of the Ecological Society of America
|September 2, 2022
PubMed
Summary

Environmental DNA (eDNA) metabarcoding effectively monitors fish biodiversity and detects invasive species in the Great Lakes. Prioritizing genetic sequencing for key species enhances eDNA accuracy for conservation and management.

Keywords:
Laurentian Great LakeseDNAearly detectionnon-indigenous speciessequence coveragespecies specificitythreatened and endangered species

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Area of Science:

  • Ecology
  • Genetics
  • Conservation Biology

Background:

  • Environmental DNA (eDNA) metabarcoding offers a powerful approach for biodiversity assessment and early detection of invasive species in aquatic ecosystems.
  • The accuracy of eDNA metabarcoding is contingent upon comprehensive reference libraries, which can be a limitation, particularly for identifying all relevant species in a region.
  • The Laurentian Great Lakes present a critical region for studying fish biodiversity and managing invasive species due to ecological and economic significance.

Purpose of the Study:

  • To evaluate the effectiveness of commonly used fish eDNA metabarcoding primer pairs in the Laurentian Great Lakes.
  • To identify critical fish species, including established and potential invasive non-indigenous species, requiring prioritized genetic sequencing for improved eDNA reference libraries.
  • To enhance the reliability of eDNA metabarcoding for fisheries conservation, management, and invasive species surveillance in the Great Lakes.

Main Methods:

  • Synthesized regional fish species lists, incorporating known indigenous and non-indigenous species identified through risk assessments.
  • Evaluated 23 commonly used fish eDNA metabarcoding primer pairs against available sequence databases for coverage and specificity.
  • Identified priority fish species for genetic sequencing to strengthen regional eDNA reference libraries.

Main Results:

  • Assessed the suitability of existing primer pairs for comprehensive fish eDNA metabarcoding in the Laurentian Great Lakes.
  • Highlighted specific established and potentially invasive non-indigenous fish species that require further genetic sequencing.
  • Provided a framework for prioritizing sequencing efforts to improve the robustness of eDNA metabarcoding for regional fisheries.

Conclusions:

  • The study provides crucial insights for optimizing eDNA metabarcoding protocols in the Great Lakes, increasing confidence in its application for conservation and management.
  • Prioritizing genetic sequencing of identified key species will significantly enhance the accuracy and utility of eDNA metabarcoding for biodiversity monitoring and invasive species early detection.
  • Integrating eDNA metabarcoding for both biodiversity assessment and invasive species surveillance is essential for effective aquatic ecosystem management.