Fishing for possum DNA

“Nothing in biology makes sense except in the light of evolution” is a reasonably  well known quote from Theodosius Dobzhansky. It makes the point that we never really understand biology until we see it through an evolutionary filter. In recent years we could play with this quote and say “Everything in biology can make sense in the light of DNA”. DNA has infiltrated its way into virtually every area of study in biology. You may not need DNA to answer your biological question but there are very few questions that are not assisted with the addition of DNA.

What does DNA have to offer? We seemed to be doing OK before it appeared on the scene after all. As I tell my students, primarily DNA is information. It can tell us about function, or timing, or change or selection or populations or – well you get the picture. For most questions in biology we always require as much information as we can. So what’s not to like?

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The protective sheath for the ‘fishing’ device.

I came relatively early to using DNA in my research. As part of my PhD in the early 90s I used sequence data to help me answer questions about the evolution of behavior and coevolution in seabirds and feather lice. Since then about half of my postgrads have used DNA to look at questions of conservation, behaviour, evolution and population management. Methods of obtaining and analyzing DNA have become a whole lot more straight-forward than the dawn of time (early 90s) and DNA is now seen as just another tool.

My neighbour here at Lincoln University, Dr James Ross, is a case in point. James has spent his career working on New Zealand’s mammalian pest species. His research usually revolves around counting, controlling or killing these pests. His tools are traps, trail cameras, tracking tunnels and waxtags. One of his chief concerns is in how to count the local population of nocturnal and secretive species like possums, stoats and rats. Counting is mostly indirect, triggered pictures on cameras, footprints left on inkpads, toothmarks on waxtags.

DNA offers a great deal of help in this sort of situation. If an animal can be made to interact with a device then you can collect DNA. Once you have DNA from multiple sources you can estimate the local population, especially when some individuals turn up on different nights (through using a mark/recapture method). Obtaining DNA can be a bit of challenge, however, but one that James is beginning to explore.

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James Ross shows how the saliva collection wax is pulled into the piping after being bitten by the possum.

Possums, on biting a waxtag, leave behind some of their DNA in their saliva. Unfortunately, DNA, when exposed to the elements, starts to degrade reasonably quickly, breaking into smaller chunks of chain, reaching a point of no useful signal within a few hours to days. Very occasionally conditions are right for preservation and DNA can persist for hundreds or even thousands of years. But the fate of most DNA dropped into the environment is to be degraded very quickly due to temperatures, humidity and micro-organisms.

James Ross and Rob Cruickshank from Lincoln University and Graham Nugent from Landcare Research, working with TBFree NZ, decided to invent a system that could be used to obtain DNA samples from possums without having to physically catch them. They needed a device that would be attractive for biting by a possum that, once bitten, was able to place the sample into a protected environment in which the DNA from the possum saliva would be safe for a day or two from degradation or subsequent visits from other possums.

After much trial an error, James and colleagues hit upon the idea of a wax blob suspended on a cord. The possum would bite the wax blob, disrupting the magnet that held the blob in place, allowing the wax blob (with the saliva DNA) to be retracted inside a protective cavity. Effectively fishing for possum DNA.

After building a stack of these devices the colleagues conducted lab trials where things seemed to work. The DNA recovered (as microsatellites) was detectable for well over a week of storage. They then moved into the field where the devices were set up in small areas of forest set near pasture. Trail cameras were placed to view what possums (and rats) did when interacting with the devices. DNA was obtained from 2/3 of the samples that were bitten. This allowed James to identify 17 individual possums. When the population was intensively trapped soon after this trial only 7 of 22 possums trapped were those that had bitten the traps. This implied that there are many possums who don’t bit waxtags but also possums that don’t get caught in traps either.

Possums are curious animals who bite most things they find in their environment, including wax blobs.

One benefit of a DNA approach was that some of the possums were detected multiple times which allowed the an estimation of the local population of 32. Given that 22 possums were later captured in traps and the DNA analysis indicated that 10 individuals were not caught at all, then the DNA mark/recapture estimate of 32 is probably very good.

While it is early days for possum fishing, this method does have a lot of possibilities. Perhaps in the future they could be used as sentinels for detecting TB infected possums (one of the main reasons for control)? Or for using genetic markers for gender to look at sex ratios? Or other genetic markers to look at age structure? In the not too distant future we may be able to put small automated gene sequencers in the field that can take the captured sample, get the sequence and then send it wirelessly to our office computer to follow possums in almost real-time. We really are getting to the point where everything in biology can make sense in the light of DNA!

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