A single‐nucleotide polymorphism‐based approach for rapid and cost‐effective genetic wolf monitoring in Europe based on noninvasively collected samples

Abstract

Noninvasive 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 noninvasively 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. We carefully selected an optimised final set of 96 SNPs (and discarded the worse half), based on assay performance and reliability. 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. 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 SNPs as a standard marker for future wildlife monitoring.

Novel efficient genome-wide SNP panels for the conservation of the highly endangered Iberian lynx

“…[15]), and (iii) their automation potential (reviewed in [16]). Finally, and contrary to what happens with STRs, SNP based assays are highly repeatable and easy to standardize across collaborators [17]. At the same time, their biallelic nature often implies lower resolution and statistical power per marker compared to the multiallelic STRs, but this can be easily counterbalanced by increasing the number of SNPs [18].…”

“…SNP discovery in non-model species, although still a major hurdle, has been greatly facilitated by recent advancements in Next Generation Sequencing (NGS) [19]. Nanoscale genetic analyses on microfluidic platforms [20] have streamlined, reduced costs, and added flexibility to the genotyping assays, minimizing at the same time the DNA quality and quantity requirements of chip-based technologies [17, 21]. Furthermore, the genotyping costs and the effort necessary to achieve the required power can be drastically reduced by selecting the most informative SNP for each particular application.…”

Genome-wide single nucleotide polymorphism (SNP) identification and characterization in a non-model organism, the African buffalo (Syncerus caffer), using next generation sequencing

“…Attention has begun to shift toward SNPs as preferred genetic markers due to their increased power of resolution and accuracy for studying fine scale population structure (Schlötterer, 2004). This is based on their high abundance throughout the genome, simple mutation characteristics, low mutation rates, usability on non-invasive samples and historical DNA, and standardization possibilities between laboratories (Kraus et al, 2014;Morin et al, 2007aMorin et al, ,b, 2004Luikart et al, 2003). SNPs have become an established marker in molecular ecology, evolutionary genetics, and animal breeding (Davey et al, 2011;Kraus et al, 2014Kraus et al, , 2012Morin et al, 2004;Santure et al, 2010).…”

Large-scale genetic census of an elusive carnivore, the European wildcat (Felis s. silvestris)

“…Unlike in many other regions, ranges of many central European species, such as large terrestrial mammals seem to be rather well known, as there is considerable public interest in their distribution and they often serve as prominent flagship species for nature conservation (Chapron et al 2014). Therefore, there is a particular focus on the distribution of this group to document and monitor occurrence, range size and population status (Frosch et al 2014;Kraus et al 2015;Simon et al 2005). In Germany, the European wildcat (Felis silvestris silvestris Schreber 1777) has become a primary target species for promoting large, connected and near-natural broad-leaf forests over the past years.…”