CSI: Ecology. Efficiency of eDNA sampling

Detecting a species from the DNA it left behind seems so much like CSI: Ecology. DNA deposited in the environment (eDNA for the cool kids), which can then be collected and identified, is increasingly advocated for ecological studies (Ficetola et al. 2008; Bohmann et al. 2014).

AdamSmart

Adam Smart: doing a bit of sampling.

Detection rates from eDNA sampling are often much higher than more traditional survey methods, which is a potentially large advantage. For example, Adam Smart, a recently-completed MSc student in QAECO with Reid Tingley as his lead supervisor, showed that invasive newts in Melbourne were detected much more frequently in a single water sample compared to a bottle trap (Smart et al. 2015).

 

While eDNA sampling can have higher detection rates than more traditional methods, it can also be more expensive. How do we determine whether eDNA sampling is cost-effective? This is the question Adam set out to answer with a second paper from his MSc, which has just been posted online (Smart et al. in press).

Adam compiled various cost data for bottle trapping and eDNA surveys. These costs included materials, travel to sites, time spent at sites, generating primers for the DNA analyses, and conducting the lab-based DNA analyses. He optimised the detection efficiency of each of the two survey methods, using our method to optimise allocation of effort among visits and effort per visit (Moore et al. 2014, but also see the latest in Moore and McCarthy in press, about which I am quite excited). He then compared the performance of the two methods as a function of different total search budgets.

eDNA_Efficiency

Probability of detection of newts at a site in Melbourne as a function of total budget  for one of the scenarios examined in Smart et al. (in press). Results are shown for high cost and low cost eDNA scenarios, and for a standard bottle trapping scenario.

It turns out that for the cases we examined, eDNA sampling and the bottle sampling had similar detection efficiencies when accounting for costs. The choice of the best method depended on the cost structures, but regardless, the efficiencies were quite similar.

 

While the two methods were similar, the cost efficiency of eDNA sampling should improve. Firstly, eDNA costs will decline over time, while the costs of traditional sampling methods are unlikely to decrease if person hours represent the main expense. Secondly, eDNA promises to detect many species simultaneously, especially for species that might be otherwise hard to detect (Bohmann et al. 2014). Thirdly, eDNA sampling avoids some of the ethical concerns arising from the effects of trapping animals.

Of course, eDNA sampling has some drawbacks. The actual source of the DNA cannot be guaranteed. Could it have arrived on the feet of ducks? Might it have arisen from contamination? Procedures exist to reduce contamination. However, DNA evidence can be nullified in law courts, so it will not be 100% reliable in ecology. Further, physical specimens might be required, in which case eDNA will not be sufficient.

However, it seems that eDNA is only set to become more prevalent. We are continuing to work on improving and evaluating eDNA sampling via an ARC Linkage Grant – CSI: Ecology here we come!

Read Adam’s paper in Methods in Ecology and Evolution, or access the submitted version here.

References

Bohmann, K. Evans, A. Gilbert, M.T.P. Carvalho, G.R. Creer, S. Knapp, M. Yu, D.W. de Bruyn M. (2014). Environmental DNA for wildlife biology and biodiversity monitoring.Trends in Ecology & Evolution, 29, 358-367. [Online]

Ficetola, G.F., Miaud, C., Pompanon, F. & Taberlet, P. (2008). Species detection using environmental DNA from water samples. Biology Letters, 4, 423–425. [Online]

Moore, A.L., McCarthy, M.A., Parris, K.M., Moore, J.L. (2014). The optimal number of surveys when detectability varies. PLoS One 9(12): e115345. doi: 10.1371/journal.pone.0115345 [Blog] [Online – open access]

Moore, A.M., and McCarthy, M.A. (in press). Optimising ecological survey effort over space and time. Methods in Ecology and Evolution. [Online] [Submitted version of manuscript] [Blog]

Smart, A.S., Tingley, R., Weeks, A.R., van Rooyen, A.R., and McCarthy, M.A. (2015). Environmental DNA sampling is more sensitive than a traditional survey technique for detecting an aquatic invader. Ecological Applications 25:1944-1952. [Online]

Smart, A.S., Weeks, A.R., van Rooyen, A.R., Moore, A.L., McCarthy, M.A., and Tingley, R. (in press). Assessing the cost-efficiency of environmental DNA sampling. Methods in Ecology and Evolution. [Online] [Submitted version of manuscript]

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About Michael McCarthy

I conduct research on environmental decision making and quantitative ecology. My teaching is mainly at post-grad level at The University of Melbourne.
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