DOI: 10.16904/envidat.661
title: Application of CRISPR-Dx and metabarcoding to catchment-level eDNA for terrestrial mammal detection

description: General description
Data associated with the publication "CRISPR-Dx and metabarcoding perform similarly for monitoring mammals with eDNA on the catchment level in high-alpine ecosystems". The data set contains the cleaned metabarcoding reads per site/catchment, the CRISPR-Dx detection per species and site, the site coordinates and a species checklist obtained from the Swiss National Park with the species known to occur at the sampling time point in the respective catchments.
 Authors
Flurin Leugger, Martina Lüthi, Michel Schmidlin, Sarah Marie-Antoine Turnheer, Zacharias Kontarakis and Loïc Pellissier
 Contact
flurinleugger@gmail.com
loic.pellissier@usys.ethz.ch
 Project description 
We collected eDNA samples in the Swiss National Park in September 2022 using VigiDNA filters. We extracted the samples in the clean lab at ETH using a modified extraction protocol of Pont et al. (2018). We used the Mamm01 primer (Tabarlet et al. 2018) for metabarcoding and for CRISPR analysis. We applied CRISPR-Dx for eight species occurring in the Swiss National Park. Additionally, we compared the eDNA detections to species inventories per catchment obtained from the Swiss National Park. See publication for more details.
 Folders
 catchments
Shape file containing the catchments sampled in the Swiss National Park.
 metadata
Folder containing files with overview of site names and extract number. Second file with metadata per site (e..g., sampling date). Column called "EVS" (Environmental sample) is the key between the two files.
 data
Folder containing a folder for eDNA and species_inventory (traditional monitoring), respectively.
 eDNA folder
CRISPR_classifications.csv: CRISPR-Dx classifications per extract (and PCR pool).
metabarcoding_seqs_all_cleaned.csv: all DNA sequences from metabarcoding after removing all sequences found in the negative controls.
 species_inventory
Species per catchment reported by the Swiss National Park, based on traditional monitoring including. visual surveys and other opportunistic records. 2: known presence in 2022, 1: maybe present in 2022, 0: not recorded in 2022
description: Resource Title: Readme.txt
 Size: 1811 bytes
 Format: text/plain
 URL: https://www.envidat.ch/dataset/7927cfd4-2861-434a-bdd3-0c3790fab6e4/resource/9aa5d934-729d-43a3-9c9f-7294dc8aa2b3/download/readme.txt
 Description: Read me file with information about files within this repository
description: Resource Title: catchments.zip
 Size: 6475 bytes
 Format: application/zip
 URL: https://www.envidat.ch/dataset/7927cfd4-2861-434a-bdd3-0c3790fab6e4/resource/f7e73ace-23c5-486b-a93e-74fb19488032/download/catchments.zip
 Description: Shape file containing the catchments sampled in the Swiss National Park
description: Resource Title: data.zip
 Size: 6818 bytes
 Format: application/zip
 URL: https://www.envidat.ch/dataset/7927cfd4-2861-434a-bdd3-0c3790fab6e4/resource/658a31d4-24d1-40f3-8468-e605c56a5dda/download/data.zip
 Description: Folder containing a folder for eDNA and species_inventory (traditional monitoring), respectively.
eDNA folder:
CRISPR_classifications.csv: CRISPR-Dx classifications per extract (and PCR pool).
metabarcoding_seqs_all_cleaned.csv: all DNA sequences from metabarcoding after removing all sequences found in the negative controls. 
species_inventory: species per catchment reported by the Swiss National Park, based on traditional monitoring including. visual surveys and other opportunistic records. 2: known presence in 2022, 1: maybe present in 2022, 0: not recorded in 2022
description: Resource Title: metadata.zip
 Size: 1102 bytes
 Format: application/zip
 URL: https://www.envidat.ch/dataset/7927cfd4-2861-434a-bdd3-0c3790fab6e4/resource/3e9d98d5-8dcf-4531-bb15-04bf3863563e/download/metadata.zip
 Description: Folder containing files with overview of site names and extract number. Second file with metadata per site (e..g., sampling date). Column called "EVS" (Environmental sample) is the key between the two files.