An Assessment of Environmental DNA as a Tool to Detect Fish Species in Headwater Streams
Summary
Proper management of species relies on accurate assessment of their distributional range. When species are rare, monitoring techniques can fail to detect them. This is particularly true in aquatic environments where the underwater environment hides organisms from view. Recent work using DNA suspended in the water column, otherwise known as environmental DNA (eDNA), has indicated that such techniques have greater sensitivity than traditional techniques in lentic systems. In this thesis, I explore the potential use of eDNA as a monitoring tool in headwater stream systems, where currents are more likely to rapidly carry suspended DNA away from the source. In Chapter 1, I provide a brief overview of the use of eDNA methods in aquatic systems [...]
Summary
Proper management of species relies on accurate assessment of their distributional range.
When species are rare, monitoring techniques can fail to detect them. This is particularly true in
aquatic environments where the underwater environment hides organisms from view. Recent
work using DNA suspended in the water column, otherwise known as environmental DNA
(eDNA), has indicated that such techniques have greater sensitivity than traditional techniques in
lentic systems. In this thesis, I explore the potential use of eDNA as a monitoring tool in
headwater stream systems, where currents are more likely to rapidly carry suspended DNA away
from the source.
In Chapter 1, I provide a brief overview of the use of eDNA methods in aquatic systems
to date. In Chapter 2 I used a stream system with an extensive history of monitoring to test
whether the pattern of detections obtained using eDNA would match the known fish communities
in this system. Due to barriers between the mainstem and tributaries, tributaries contained subsets
of the species present in the mainstem. I used this situation to test whether I would see false
negative and/or false positive results using eDNA. Though eDNA detected species where they
were known to be present, it also detected species where they were absent. This result may be
due to low level contamination and/or movement of DNA by vectors such as piscivorous
vi
organisms. I conclude that a cautious approach to interpretation of eDNA results should be
employed.
In Chapter 3, I introduced caged fish into two otherwise fishless headwater streams and
took eDNA samples at evenly spaced intervals downstream of the cage. I repeated this 19 times
from mid-summer through autumn, over flows ranging from approximately 1 to 96 l/sec. I used
quantitative PCR to relate DNA copy number to distance from source for each of these 19
sampling events. I found a wide range of patterns in the DNA levels downstream of the cages,
ranging from a rapid initial decline to a near flat line. In all cases I had detectable DNA at 240 m
from the cage, even over a near 100 fold increase in flows. Though increasing flows generally
reduced DNA levels near to the cage, they had relatively little effect at downstream sites.
Additionally, I found that the presence of leaf biomass during the fall period could completely
erase otherwise high DNA levels.
