A reading of the first paragraph of the ‘Results’ from the Piggott et al paper states that “…112 of 170 (65.8%) putative fox faeces yielded 3, 4 or 5 locus genotypes. In total, 39 scats (22.9%) failed to amplify for any locus and 19 of 170 (11.2%) could only be genotyped at one or two loci.”
So 112 scats with >3 locus genotypes; 19 scats with 1 or 2 locus genotypes and 39 scats that failed to amplify; a total of 170 scats. They identified 54 different foxes by genotype from 112 scats with >3 loci (their cut-off). That is, some of those 54 different foxes did more than one poo! Quite a possibility really.
So getting back to the angst in Dr Peacock’s comments, I believe it is you, Dr Peacock, who has misread this paper. Only 39 of 170 scats (22.9%) failed to satisfactorily amplify any microsatellite DNA markers and 58 of 170 scats (34%) were excluded from their analysis. I consider 65.8% is far better DNA recovery than 20% (5 of 25 scat) from mitochondrial (maternal origin) DNA used for fox identification by the Invasive Animals CRC. By all means Dr Peacock please run another one of your Chi squared tests on these numbers.
The CRC molecular scientist Dr Oliver Berry originally used mitochondrial DNA and perhaps still does. So it says on he site - http://www.foxdna.animals.uwa.edu.au/welcome/aims_and_approach
The micro-satellite DNA assay methods used and developed by Maxine Piggott years back is more powerful as a genomic marker. Please correct me if I am in error.
And Dr Peacock, please tell us about the relative merits in using genomic microsatellite markers versus mitochondrial DNA markers in Tasmania for fox field forensics?
Congratulations to Monash University and to the Victorian collaborators who had the ‘proof of concept’ vision and kicked this work off well over a decade and a half age ago. They saw it through without IA CRC support. Dr Nick Robinson at La Trobe University started this work back in the late 1980s when he and his colleagues first used DNA primers in fox studies.
This careful research approach shows that fox scat DNA can determine the actual population size of foxes in an area from independent samples (scat) as well as animals active at bait stations. Cyanide ejectors, used in the Piggott et al study, was a way to collect the dead foxes so as to match their bodies with field collected scats. Perhaps the potential of DNA surveys of this elegance to measure control efficacy has not dawned on Dr Peacock. It offers a ‘population size’ survey technique; currently the best available.
Dr David Obendorf
I AM compelled to defend the article published on Tasmanian Times on Monday 23 March: Forensic Scatology - collect enough shit: Here . In particular reply to Dr Tony Peacock’s three comments posted at 12.38 pm, 12.56 pm and 2.22 pm yesterday.