Raw sequencing data and ngsfilters for snow track eDNA samples

<p>Continued advancements in environmental DNA (eDNA) research have made it possible to access intraspecific variation from eDNA samples, opening new opportunities to expand non-invasive genetic studies of wildlife populations. However, the use of eDNA samples for individual genotyping, as typically performed in non-invasive genetics, still remains elusive. We present the first successful individual genotyping of eDNA obtained from snow tracks of three large carnivores: brown bear (<em>Ursus</em> <em>arctos</em>), European lynx (<em>Lynx</em> <em>lynx</em>) and wolf (<em>Canis</em> <em>lupus</em>). DNA was extracted using a protocol for isolating water eDNA and genotyped using amplicon sequencing of short tandem repeats (STR) and, for brown bear, a sex marker, on a high-throughput sequencing platform. Individual genotypes were obtained for all species, but genotyping performance differed among samples and species. The proportion of samples genotyped to individuals was higher for brown bear samples (5/7) than for wolf (7/10) and lynx (4/9), but locus genotyping success was greater for brown bear (0.88). Results for three species show that reliable individual genotyping, including sex identification, is now possible from eDNA in snow tracks, underlining its vast potential to complement the non-invasive genetic methods used for wildlife. To fully leverage the application of snow track eDNA, improved understanding of the ideal species- and site-specific sampling conditions, as well as laboratory methods promoting genotyping success are needed. This will also inform efforts to retrieve and type nuclear DNA from other eDNA samples, thereby advancing eDNA–based individual and population-level studies.</p>