Noninvasive genetic sampling of two flying fox species provides a high rate of genotyping success and a low error rate during amplification

Noninvasive genetic sampling techniques are useful tools for providing genetic data that are crucially needed for determining suitable conservation actions. Yet these methods may be highly unreliable in certain situations for instance, when working with faecal samples of frugivorous species in tropical areas. In this study, we tested the applicability of noninvasive genetic sampling on two Comoro Islands flying fox species: Pteropus livingstonii and P.seychellensis comorensis in order to optimize the sampling and laboratory process. Both mitochondrial (mtDNA) and microsatellite markers were tested using two common faeces conservation protocols (ethanol and silica gel), and the polymerase chain reaction (PCR) success and genotyping error rates were assessed. The average proportion of mtDNA PCRs positive results was 55% for P.livingstonii and 38% for P.s.comorensis, and higher amplification success was obtained for samples preserved in ethanol as compared to silica gel. The average genotyping success rate was high (74% for P.livingstonii and 95% for P.s.comorensis) and the genotyping error rate was low for both species. Despite our results confirm the effectiveness of using noninvasive genetic sampling methods to study flying fox species, the protocol we used can be optimized to provide higher efficiency. Some recommendations related to field sampling protocols and laboratory methods are proposed in order to optimize amplification rate and minimize genotyping errors.