Biological Invasions

, Volume 20, Issue 2, pp 299–314 | Cite as

Development of environmental DNA (eDNA) methods for detecting high-risk freshwater fishes in live trade in Canada

  • Mélanie Roy
  • Valérie Belliveau
  • Nicholas E. Mandrak
  • Nellie Gagné
Original Paper


Preventing the arrival, establishment, and spread of aquatic invasive species is an important step in protecting our aquatic environments. The use of detection tools, like DNA barcoding technologies, high-throughput sequencing and environmental DNA (eDNA) monitoring, is becoming increasingly important in preventing the introduction of potential invasive species. The combination of eDNA with realtime PCR (qPCR) provide the opportunity to have a rapid and specific detection. In this study, we developed a DNA sequence library that has sufficient depth and species coverage such that high-risk species can be confidently discriminated from legitimately imported and native species. A total of 12 species-specific qPCR assays were developed for the detection of 13 potential invasive species (pAIS) in bulk water samples. Detection of these species was also compared with a HTS approach. We have demonstrated the high sensitivity of qPCR assays using eDNA at very low densities, suggesting we could detect a low number of individuals mixed with non-target species in a simulated live shipment. For the detection of a targeted list of species, qPCR is advantageous. The mini-barcodes developed in this project offered a good sensitivity of detection, and HTS is a discovery tool that can be desirable when unlisted or numerous species need to be identified.


Aquatic invasive species High-throughput sequencing DNA barcoding Real-time PCR detection Pet and live food trade RHO COI 



Funding for this project was provided by the Genomics Research & Development Initiative from the Government of Canada. We sincerely thank the Royal Ontario Museum, Francis Leblanc, Valérie Godbout and Charlotte Schoelinck for their technical support and advice, and various collaborators and museums that provided samples.


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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Mélanie Roy
    • 1
  • Valérie Belliveau
    • 1
  • Nicholas E. Mandrak
    • 2
  • Nellie Gagné
    • 1
  1. 1.Gulf Fisheries CenterFisheries and Oceans CanadaMonctonCanada
  2. 2.Department of Biological SciencesUniversity of Toronto ScarboroughTorontoCanada

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