Our purpose was to identify an experimental procedure using PCR that p
rovides a reliable genotype at a microsatellite locus using only a few
picograms of template DNA. Under these circumstances, it is possible
(i) that one allele of a heterozygous individual will not be detected
and (ii) that PCR-generated alleles or 'false alleles' will arise. A m
athematical model has been developed to account for stochastic events
when pipetting template DNA in a very dilute DNA extract and computer
simulations have been performed. Laboratory experiments were also carr
ied out using DNA extracted from a bear feces sample to determine if e
xperimental results correlate with the mathematical model. The results
of 150 typing experiments are consistent with the proposed model. Bas
ed on this model and the level of observed false alleles, an experimen
tal procedure using the multiple tubes approach is proposed to obtain
reliable genotypes with a confidence level of 99%. This multiple tubes
procedure should be systematically used when genotyping nuclear loci
of ancient or forensic samples, museum specimens and hair or feces of
free ranging animals.