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Reliable microsatellite genotyping of the badger using faecal DNA
Journal
Molecular Ecology,
Volume 12,Number 6, June 2003, pp. 1649-1661(13)
Blackwell Publishing
Authors
Frantz A.C.; Pope L.C.; Carpenter P.J.; Roper T.J.;
Wilson G.J.; Delahay R.J.; Burke T.
Abstract
The potential link between badgers and bovine
tuberculosis has made it vital to develop accurate techniques to census
badgers. Here we investigate the potential of using genetic profiles
obtained from faecal DNA as a basis for population size estimation.
After trialling several methods we obtained a high amplification success
rate (89%) by storing faeces in 70% ethanol and using the guanidine
thiocyanate/silica method for extraction. Using 70% ethanol as a storage
agent had the advantage of it being an antiseptic. In order to obtain
reliable genotypes with fewer amplification reactions than the standard
multiple-tubes approach, we devised a comparative approach in which
genetic profiles were compared and replication directed at similar, but
not identical, genotypes. This modified method achieved a reduction in
polymerase chain reactions comparable with the maximum-likelihood model
when just using reliability criteria, and was slightly better when using
reliability criteria with the additional proviso that alleles must be
observed twice to be considered reliable. Our comparative approach would
be best suited for studies that include multiple faeces from each
individual. We utilized our approach in a well-studied population of
badgers from which individuals had been sampled and reliable genotypes
obtained. In a study of 53 faeces sampled from three social groups over
10 days, we found that direct enumeration could not be used to estimate
population size, but that the application of mark–recapture models has
the potential to provide more accurate results.
Keywords
bovine tuberculosis; mark–recapture models;
maximum-likelihood model; molecular scatology; multiple-tubes approach;
population size estimation
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