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

Citation

Schultz, Anthony J. et al. (2018), Data from: Fresh Is best: accurate SNP genotyping from koala scats, Dryad, Dataset, https://doi.org/10.5061/dryad.mq0gb

Abstract

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.

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