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Fish Survey Database

GEN-FISH collaborators designed, tested, and validated 183 CO1 assays and 175 Cyt-b assays, covering 80% of all freshwater fish species in Canada. We additionally developed 5 taxonomic and 9 regional OpenArray chips for rapid eDNA surveys. We tested these assays through 17 partner-lead case studies and our “500-Waterbody” project, sampling 1,204 sites in the first and largest pan-national eDNA survey of its kind.

Explore the eDNA sampling map below to get a sense of which species are present throughout Canada.

The broader GEN-FISH community caught some data errors in our eDNA Sampling Map, so we’re taking a look now!

eDNA ASSAY DATABASE

The vast majority of eDNA assays that were developed through GEN-FISH were designed and tested by students! These early career professionals are in the process of completing their theses and publishing their results—when everyone has had a chance to publish, the full assay database will be made available here. 

For each assay, the following information will be provided:

  • Common name (Mandrak et al. 2023)
  • Species Name (Mandrak et al. 2023)
  • Previous Species Name (If Different)
  • GEN-FISH ID # (Order.Family.Species)
  • Comments on Species (e.g., “Arctic Lamprey is similar or indistinguishable from American Brook Lamprey and Darktail Lamprey; single assay for all three”)
  • Lab Group
  • Assay Designer (Name)
  • Target Gene (CO1, Cyt-b
  • Developed for OpenArray? (Yes or No)
  • Type of Assay (SYBR, TaqMan, both)
  • Type of TaqMan (MGB, TAMRA, QSY)
  • Assay designed for multiple species? (Yes or No)
  • Species Designed For (List)
  • Assay Name (From ThermoFisher)
  • Forward Primer Name
  • Forward Primer Sequence
  • Reverse Primer Name
  • Reverse Primer Sequence (5′-3′)
  • Probe Name
  • Probe Sequence
  • Dye Used for Probe
  • # Forward Primer Mismatches
  • # Reverse Primer Mismatches
  • # Probe Mismatches
  • Total Number of Mismatches (#F + #R + #P = #Total)
  • Amplicon Length (bp)
  • Annealing Temperature (ºC)
  • Species Tested On (In-Vitro)
  • Cross-reactivity (Species list; provide specifics/thresholds in the Notes)
  • Tissue Information (Number of individuals, synthetic/tissue-derived DNA, etc.)
  • Biogeographic Zone Tested In-Vitro (e.g., Pacific Ocean, Arctic Ocean, Gulf of Mexico, Hudson Bay, Great Lakes, Atlantic Ocean)
  • GenBank Accession Number(s) for Target Species
  • Alignment Files
  • Assay Design Software (Name)
  • Notes
  • GEN-FISH Publications
  • Other Publications
OTHER ENVIRONMENTAL DNA RESOURCES
Infographic showing different factors that influence eDNA collection
Uses and Limitations of eDNA in Fisheries Management

The Great Lakes Fishery Commission (GLFC) Science Transfer Program team, including GEN-FISH member Dr. Margaret Docker, developed this eDNA toolkit to provide fishery managers an objective understanding of the potential uses and limitations of eDNA surveillance, and the tradeoffs of employing eDNA over more traditional survey methods. Explore these products for an overview of the basics:

Improving eDNA Reliability for Resource Management

GEN-FISH members and partners also collaborated to develop another GLFC Science Transfer Program tool: the eDNA Decision Checklist. This checklist is designed to support managers who are:

  • Designing eDNA surveys
  • Training field crews who will be performing eDNA sampling
  • Selecting an eDNA lab to work with
  • Determining what information to request from eDNA labs
  • Interpreting the reliability of reported eDNA results

Give this interactive checklist a try to generate a custom Submission Report for your eDNA project, or see the static checklist here: eDNA Decision Checklist – static.