Testing the effectiveness of genetic monitoring using genetic non-invasive sampling

1. Effective conservation requires accurate data on population genetic
diversity, inbreeding, and genetic structure. Increasingly, scientists are
adopting genetic non-invasive sampling as a cost-effective population-wide
genetic monitoring approach. Genetic non-invasive sampling has, however,
known limitations which may impact the accuracy of downstream genetic
analyses. 2. Here, using high quality SNP data from blood/tissue sampling
of a free-ranging koala population (n = 430), we investigated how the
reduced SNP panel size and call rate typical of genetic non-invasive
samples (derived from experimental and field trials) impacts the accuracy
of genetic measures, and also the effect of sampling intensity on these
measures. 3. We found that genetic non-invasive sampling at small sample
sizes (14% of population) can provide accurate population diversity
measures, but slightly underestimated population inbreeding coefficients.
Accurate measures of internal relatedness required at least 33% of the
population to be sampled. Accurate geographic and genetic spatial
autocorrelation analysis requires between 28% and 51% of the population to
be sampled. 4. We show that genetic non-invasive sampling at low sample
sizes can provide a powerful tool to aid conservation decision-making and
provide recommendations for researchers looking to apply these techniques
to free-ranging systems.