Data from: More affordable and effective noninvasive SNP genotyping using high-throughput amplicon sequencing

Non-invasive genotyping methods have become key elements of wildlife
research over the last two decades, but their widespread adoption is
limited by high costs, low success rates, and high error rates. The
information lost when genotyping success is low may lead to decreased
precision in animal population densities, which could misguide
conservation and management actions. Single nucleotide polymorphisms
(SNPs) provide a promising alternative to traditionally used
microsatellites as SNPs allow amplification of shorter DNA fragments, are
less prone to genotyping errors, and produce results that are easily
shared among laboratories. Here, we outline a detailed protocol for
cost-effective and accurate noninvasive SNP genotyping using multiplexed
amplicon sequencing optimized for degraded DNA. We validated this method
for individual identification by genotyping 216 scats, 18 hairs and 15
tissues from coyotes (Canis latrans) using 26 SNPs. Our genotyping success
rate for scat samples was 93%, and 100% for hair and tissue, representing
a substantial increase compared to previous microsatellite-based studies
while remaining at a low cost of under $5 per PCR replicate (excluding
labor). The accuracy of the genotypes was further corroborated in that
genotypes from scats matching known, GPS-collared coyotes were always
located within the territory of the known individual. We also show that
different levels of multiplexing produced similar results, but that PCR
product cleanup strategies can have substantial effects on genotyping
success. By making noninvasive genotyping more affordable, accurate, and
efficient, this research may allow for a substantial increase in the use
of noninvasive methods to monitor and conserve free-ranging wildlife
populations.