Data from: Fresh Is best: accurate SNP genotyping from koala scats

Maintaining genetic diversity is a crucial component in conserving
threatened species. For the iconic Australian koala, there is little
genetic information on wild populations that is not either skewed by
biased sampling methods (e.g. sampling effort skewed towards urban areas)
or of limited usefulness due to low numbers of microsatellites used. The
ability to genotype DNA extracted from koala scats using next-generation
sequencing technology will not only help resolve location sample bias but
also improve the accuracy and scope of genetic analyses (e.g. neutral
versus adaptive genetic diversity, inbreeding, and effective population
size). Here we present the successful SNP genotyping (1272 SNP loci) of
koala DNA extracted from scat, using a proprietary DArTseq™ protocol. We
compare genotype results from two day old scat DNA and 14 day old scat DNA
to a blood DNA template, to test accuracy of scat genotyping. We find that
DNA from fresher scat results in fewer loci with missing information than
DNA from older scat, however, 14 day old scat can still provide useful
genetic information, depending on the research question. We also find that
a subset of 209 conserved loci can accurately identify individual koalas,
even from older scat samples. In addition, we find that DNA sequences
identified from scat samples through the DArTseq™ process can provide
genetic identification of koala diet species, bacterial and viral
pathogens, and parasitic organisms.