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Fox scat on tussock grass, Charlottes Pass, Kosciuszko National Park

The precision and sensitivity of DNA ‘fingerprinting’ has been well established. It has been used to convict individuals in serious cases such as homicide or rape.

Since 2005 the Tasmanian Fox Program has collected 58 scats that for one reason or another contained ‘fox’ DNA.

A scat with ‘fox ‘DNA in it is designated a “fox scat”; many people would be content to leave it at that. After all, we have all become accustomed to hearing about the astronomical odds against DNA profiles being in error. It is tempting to believe that the fox scat DNA test must be as good as flawless.

Let’s examine why this assumption is a bridge too far.

As previous articles have highlighted, and now corroborated by the new Fox Program manager, there is nothing that links any of these scats to the Tasmanian landscapes or to each other. No two scats are known to be produced by the same fox. Put simply, the amplification of fox DNA in field collected scats cannot be directly assumed to be defecated by a Tasmanian fox without some extra diligence – a few more steps that have so far alluded us.

No one has ever bothered to prove the provenance of these scat exhibits – their diagnosis as turds produced by foxes is only based on the presence of amplified fox DNA sequences.

Any implied conclusions that you may feel willing to draw from fox positive DNA results, can only be made if there is no other source of fox DNA in the Tasmanian environment other than that produced by Tasmanian foxes.  Because if you import fox DNA and use it on a routine basis you’re asking for contamination trouble.

The Fox Program has imported fox turds in large quantities over several years – it is claimed for training scent dogs and ensuring that the dogs will find such scats in field situations. In these circumstances the risk of DNA-contamination is heightened and the necessity to use demonstrable aseptic technique paramount if contamination is to be avoided.

DNA contamination happens in laboratories and it is not uncommon. It is quite understandable too, because in theory all you need is a single cell with foreign DNA to end up in the wrong place.  That’s a single cell that cannot be seen with the naked eye.  In fact you would need a powerful microscope to see it even if you knew where to look for it.  What’s more, you would not know that it was a source of contamination until after you did the test.

Does DNA-contamination happen in the field? Of course it can, but it cannot be detected very easily - if at all. 

Even the fox-scat testing laboratory in Canberra has had problems with DNA-contamination that resulted in that facility closing for decontamination. However, in the case of genetics testing labs, the problem can be detected!  This is the key difference. In the field where the standard of aseptic technique is much lower and the chance of contamination probably much higher, contamination cannot be detected.

And that’s the bitter irony. If scats contaminated with fox DNA are tested in the laboratory, they all of a sudden become fox scats.  Hey Presto! They become fox scats from a Tasmanian fox with high precision! In effect, the laboratory has leant its confidence to the field practices whether it is deserved or not. Because how could the laboratory know if the scats were contaminated or genuine? They can’t.

The chances of DNA-contamination MUST exist if people are handling fox DNA on a routine basis and working in an environment that might be contaminated with it. Under these circumstances it is almost inevitable that some of many thousands of samples will be DNA-fox positive via error.

Let’s put this in a more familiar CSI scenario.

Can you imagine the team using scrupulous laboratory techniques to DNA profile blood taken from a site where the same team has also sprinkled the suspect’s blood around – to test their ability to detect the suspect’s blood?  It would seem a bit stupid wouldn’t it? But if the lab didn’t know this, what would they be concluding? 

How long would it take to have the case dismissed by a judge – seconds or minutes?

The Fox Program is aware of the risk of DNA-contamination in the field and through their chain of custody; it claims to have protocols in place to minimise the risk of DNA-contamination.

But it was totally silly to import fox turds as they did. This decision jeopardised the credibility of the fox-DNA test as the definitive test for confirming the presence of foxes in Tasmania. Remember, the accuracy of the fox-DNA test is not in question, but the risk of DNA-contamination of field-collected samples cannot and has not been discounted.

Interestingly, none of the “independent” reviews of the Tasmanian fox program have mentioned the risk of contamination and it’s impact upon confidence in the scat DNA test.  To them, a scat with fox DNA in it is designated a “fox scat”; it’s as simple as that. Even when vast quantities of fox DNA have been sent over from the mainland in a process that seemed somewhat ad hoc.

As always, the devil is in the details when it comes to the claimed accuracy of anything. The fox may not necessarily be in the crap either!

DNA-contamination would explain the very unusual scat DNA data provided by DPIPWE. It is one of the best hypotheses on offer, yet it’s hard to contend with the magnitude of such contamination as being accidental. Yet without absolutely scrupulous and transparent scat collection methods a more disturbing possibility can’t be discounted either.