Data from: A SNP-based approach for rapid and cost-effective genetic wolf monitoring in Europe based on non-invasively collected samples

Non-invasive genetics based on microsatellite markers has become an indispensable tool for wildlife monitoring and conservation research over the past decades. However, microsatellites have several drawbacks, such as the lack of standardisation between laboratories and high error rates. Here we propose an alternative Single Nucleotide Polymorphism (SNP) based marker system for non-invasively collected samples, which promises to solve these problems. Using nanofluidic SNP genotyping technology (Fluidigm) we genotyped 158 wolf samples (tissue, scats, hairs, urine) for 192 SNP loci selected from the Affymetrix v2 Canine SNP Array. Based on assay performance and reliability we selected an optimised final set of 96 SNPs. We found rates of missing data in this SNP set of <10% and genotyping error of ~1%, which improves genotyping accuracy by nearly an order of magnitude when compared to published data for other marker types. Further, we evaluated assay specificity by cross-species testing and statistical power by population structure analysis. Our approach provides a tool for rapid and cost-effective genotyping of noninvasively collected wildlife samples. The ability to standardise genotype scoring combined with low error rates promises to constitute a major technological advancement and could establish as a standard marker for future wildlife monitoring.