Fresh is best: Accurate SNP genotyping from koala scats

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 toward 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 vs. 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.

A genomic approach to inferring kinship reveals limited intergenerational dispersal in the yellow fever mosquito

“…For example, monitoring of rare mammals is often carried out by the scats they leave, with recent work using DNA from scats to infer N e from kinship (Skrbinšek et al, 2012). As methods for retrieving DNA from scats improve (Schultz, Cristescu, Littleford-Colquhoun, Jaccoud, & Frère, 2018), investigating kin networks and intergenerational dispersal with high-density markers may become increasingly viable for achieving conservation objectives.…”

A genomic approach to inferring kinship reveals limited intergenerational dispersal in the yellow fever mosquito

“…For example, monitoring of rare mammals is often carried out by the scats they leave, with recent work using DNA from scats to infer Ne from kinship (Skrbinšek et al, 2012). As methods for retrieving DNA from scats improve (Schultz, Cristescu, Littleford-Colquhoun, Jaccoud, & Frère, 2018), investigating kin networks and intergenerational dispersal with high density markers may become increasingly viable for achieving conservation objectives.…”

Museum specimens provide reliable SNP data for population genomic analysis of a widely distributed but threatened cockatoo species

“…This is especially so for endangered or rare species and those with widespread distributions (Payne & Sorenson, 2002;Piggott & Taylor, 2003). Population parameter estimates risk being inaccurate or misinformative due to a lack of samples or skewed due to insufficient geographic sampling (Hale, Burg, & Steeves, 2012;Schultz, Cristescu, Littleford-Colquhoun, Jaccoud, & Frère, 2018). Furthermore, conservation genomic studies investigating genetic changes in a species/population over time often rely on long-term sampling projects or access to historical samples (Wandeler, Hoeck, & Keller, 2007).…”