False alleles derived from microbial DNA pose a potential source of error in microsatellite genotyping of DNA from faeces

Microsatellite genotyping of wild animals using DNA extracted from noninvasive samples such as faeces is a powerful means to identify individuals within a population and examine aspects of genetic social structure, such as relatedness and paternity. However, the use of the low quantities of poor quality DNA typically obtained from noninvasive samples can result in genotyping errors. Here we report the first instance of artefactural 'alleles' resulting from specific co-amplification of microorganismal DNA present in the total DNA derived from faeces.