For monitoring wildlife, genotyping DNA from noninvasively collected samples is a widely used method. However, the degraded and low quantity of DNA often recovered from such samples make it hard to obtain high quality genotypes, especially for microsatellites. We demonstrate the applicability of SNP-typing from noninvasive samples to monitor wildlife in two different species - tigers (Panthera tigris) and the Caribbean Queen conch (Strombus gigas).
We designed primers targeting about a hundred SNPs for both tigers and conch. The genotyping protocol involves a simple multiplex PCR where all targets are amplified in a single reaction. The products from each sample are barcoded and pooled before sequencing. Using this protocol we genotyped noninvasively collected tiger samples such as feces, hair and saliva. Using this data (~100 SNPs), we were able to identify unique individuals, discern relatedness between individuals, and detect population structure. We also genotyped conch fritters from restaurants along with some field-collected samples. We were able to detect population structure and identify related individuals.
Our study provides a proof-of-concept for a rapid, cost-effective, accurate and scalable method that can applied to conservation scenarios. Less...