MICROSATELLITE SCORING ERRORS ASSOCIATED WITH NONINVASIVE GENOTYPING BASED ON NUCLEAR-DNA AMPLIFIED FROM SHED HAIR

In the context of a study of wild chimpanzees, Pan troglodytes verus, we found that genotypes based on single PCR amplifications of microsat ellite loci from single shed hair have a high error rate. We quantifie d error rates using the comparable results of 791 single shed hair PCR amplifications of 11 microsatellite loci of 18 known individuals. The most frequent error was the amplification of only one of the two alle les present at a heterozygous locus. This phenomenon, called allelic d ropout, produced false homozygotes in 31% of single-hair amplification s. There was no difference in the probability of preferential amplific ation between longer and shorter alleles. The probability of scoring f alse homozygotes can be reduced to below 0.05 by three separate amplif ications from single hairs of the same individual or by pooling hair s amples from the same individual. In this study an additional 5.6% of t he amplifications gave wrong genotypes because of contamination, label ling and loading errors, and possibly amplification artefacts. In cont rast, amplifications from plucked hair taken from four dead individual s gave consistent results (error rate < 0.01%, n = 120). Allelic dropo ut becomes a problem when the DNA concentration falls below 0.05 ng/10 PL in the template as it can with shed hair, and extracts from faeces and masticated plant matter.