Environmental DNA and detec2on of invasive finfish in BC lakes Davon Callander1, Ma=hias Herborg2, Cathryn Abbo=1 1 Pacific Biological Sta.on, Fisheries and Oceans Canada, Nanaimo BC 2 Aqua.c Invasive Species Coordinator, Ministry of Environment Traditional identification
Ecosytems
•  Rich diversity of species
•  Rich diversity of DNA
•  Naturally occurring genetic
material
Environmental DNA
•  Source
–  Sloughed cells
–  Excreted
–  Reproduction
–  Free floating DNA or inside cells
Environmental DNA
Laramie, USGS
eDNA Process ?
Adapted from Mächler et al, 2014
DNA Barcode
Short DNA sequence
Standardized genetic region
Enables species discrimination
DNA Metabarcoding
•  Bulk, complex, samples
–  Ethanol from insect traps
–  Gut contents
–  Leech’s blood
–  Soil/benthos
–  Water
Laramie, USGS
eDNA Detection – 2 pathways
•  Passive
–  What species live here?
•  Biosurveillance
•  Early detection of invasives
•  Monitor secondary spread
NGS
metabarcoding
•  Active
–  Is Sp X here?
–  Presence/Absence (not detected)
•  Targeted sampling for specific species
qPCR
Metabarcoding (NGS)
qPCR
When do we use eDNA?
Detection
Field
sampling
more cost
effective
eDNA sampling more
cost effective
eDNA
sampling
AIS early
detection!
Effort
High population
density
Low population
density
Large body size
Small body size
Adapted from Goldberg
Conventional vs eDNA
• 
• 
• 
• 
• 
• 
• 
Standardised sampling
High sensitivity
Non invasive
ID all stages
Mutli species detection
Retroactive addition of taxa
No observation/detection bias
• 
• 
• 
• 
No permits required
Low pathogen transfer risk
Unrestricted timing
Low equipment needs
•  Abundance & proximity
data
Challenges
[eDNA] = rate production - rate degradation
Production
•  Fish density
•  Fish health
•  Reproductive status
•  Metabolism
Degradation
•  UVB exposure
•  Habitat
•  Water temp
•  Adsorption
•  pH
•  Water volume
Challenges
Contamination
Site
Field
Laboratory
Analysis
Project goals (1) Biosurveillance
•  eDNA to detect invasive finfish in BC lakes.
–  Develop molecular aspects of metabarcoding tool
•  Universal fish primers
•  Multiple genes à better taxonomic resolution
–  Test sampling design for lakes
Lake Sampling
•  Is eDNA ubiquitously
distributed in/around lake?
–  Regions of lake
–  Adjacent sites
–  Large/small lakes
•  Seasonal detection variability
•  Thermocline eDNA barrier?
Project goals (1) Biosurveillance
•  eDNA to detect invasive finfish in BC lakes.
–  Compare effectiveness of tool w/ known lake
biodiversity
–  Use tool to assess sp assemblages in lakes
•  new AIS incursions, 2° spread, native sp
–  Include zebra/quagga mussel monitoring
Project goals (2) Rapid response
•  Targeted species detection
–  Yellow Perch
–  Northern Pike
–  Zebra/quagga mussel
– Small Mouth Bass
– Large Mouth Bass
–  Tech transfer & Analytical validation
–  Development of new molecular markers
•  Investigate AIS reports, 2° spread
•  Assess eradication success
Perspectives
•  Molecular methods
•  Costs
•  Contamination and controls
•  Quantitative aspect
•  Test validity in highly diverse regions
Thank you
[email protected]
Conventional Methods
eDNA
--
ü
Low-Med
Very High
Invasiveness
High
Low
ID all stages
--
ü
Multi species detection
--
ü
Retroactive addition of taxa
--
ü
Observer and detectability bias
High
Low
Permitting required
Yes
--
Pathogen transfer risk
High
Low
Restricted
Unrestricted
Special equipment required
Yes
--
Safety equipment required
High
Low
Abundance and proximity data
Yes
--
Standardised sampling
Sensitivity
Timing