DOI: 10.5061/dryad.9kd51c5q1
title: Raw sequencing data and ngsfilters for snow track eDNA samples

description: 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.
description: Snow tracks of brown bear, lynx and wolf were collected
 opportunistically during winter in 2019, 2020 and 2022 in the Slovenian
 Alps and Dinaric Mountains (seven brown bear samples and nine lynx
 samples) and in the French Alps (ten wolf samples). For genotyping of each
 species, we used a set of STR markers designed for optimal multiplex
 amplification and HTS genotyping. The brown bear set includes 13 STR
 recently described and used for individual profiling from fecal DNA, with
 the addition of a sex-specific marker. For wolf and lynx, we used 13 new
 STRs. We performed sequencing on a NovaSeq platform (2x150 bp) (libraries
 with id DIVJA088, DIVJA089, DAB074) and on a Miniseq platform (2x150 bp)
 (library LF22). Amplicons were sequenced in multiplexes, and necessary
 information for demultiplexing is in .ngsfilter files.
description: # Raw sequencing data and ngsfilters for snow track eDNA samples
 [https://doi.org/10.5061/dryad.9kd51c5q1](https://doi.org/10.5061/dryad.9kd51c5q1) ## Description of the data and file structure The dataset contains four libraries with STR amplicons for three carnivore species: DIVJA088 (brown bear), DIVJA089 (brown bear), DAB074 (brown bear, wolf and lynx), LF22 (wolf). Besides raw reads, the ngsfilter file is attached to each library. Ngsfilter is used for further data processing and contains information about sample name, sample position on plate, primers and tags sequences. More details about mulitplexing concept can be found in De Barba et al., 2017. **De Barba, M., Miquel, C., Lobréaux, S., Quenette, P. Y., Swenson, J. E., & Taberlet, P. (2017). High-throughput microsatellite genotyping in ecology: Improved accuracy, efficiency, standardization and success with low-quantity and degraded DNA. Molecular Ecology Resources, 17(3), 492–507.** ## Code/Software To process the data see the description of the pipeline in https://github.com/PazhenkovaEA/ngs\_pipelines.py