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A single‐nucleotide polymorphism‐based approach for rapid and cost‐effective genetic wolf monitoring in E urope based on noninvasively collected samples
Author(s) -
Kraus Robert H. S.,
vonHoldt Bridgett,
Cocchiararo Berardino,
Harms Verena,
Bayerl Helmut,
Kühn Ralph,
Förster Daniel W.,
Fickel Jörns,
Roos Christian,
Nowak Carsten
Publication year - 2015
Publication title -
molecular ecology resources
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.96
H-Index - 136
eISSN - 1755-0998
pISSN - 1755-098X
DOI - 10.1111/1755-0998.12307
Subject(s) - genotyping , biology , snp , single nucleotide polymorphism , snp genotyping , microsatellite , molecular inversion probe , genotype , genetics , computational biology , snp array , genetic marker , allele , gene
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 ( F luidigm), we genotyped 158 wolf samples (tissue, scats, hairs, urine) for 192 SNP loci selected from the A ffymetrix v2 Canine SNP Array. We carefully selected an optimised final set of 96 SNP s (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 SNP s as a standard marker for future wildlife monitoring.