Raw sequencing data and ngsfilters for snow track eDNA samples

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 (Ursus arctos), European
lynx (Lynx lynx) and wolf (Canis lupus). 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.