Field-based eDNA analysis to detect the threatened and elusive African manatee

Data associated to the publication "Rapid field-based detection of a threatened and elusive species with environmental DNA and CRISPR-Dx"
Authors:
Flurin Leugger, Martina Lüthi, Michel Schmidlin, Zacharias Kontarakis and Loïc Pellissier
Contact:
flurinleugger@gmail.com loic.pellissier@usys.ethz.ch
Project description:
We collected eDNA samples in the Conkouati-Douli National Park in the Republic of Congo in 2023 in collaboration with Beauval Nature and HELP Congo. We analyzed the samples on site in the national park using CRISPR-Dx assays to detect the African manatee (Trichechus senegalensis). Additionally, we transported the remaining samples (buffer) to Switzerland and used a high-sensitivity protocol with CRISPR-Dx assays and a qPCR assay to verify the field-based detections. The qPCR of Hunter et al. (2018) detects the genus manatee (Trichechus). See publication for more details (doi will be added after publication).
Folders:
lateral_flow_tests_images\:
Images of the lateral flow tests used to analyze the eDNA extracts in the national park. File names correspond to the site names. At each site, we took two filter replicates. We ran 8 PCRs per filter/extract and pooled two PCRs together, resulting in 4 CRISPR-Dx assays per extract. The EVE number on top of the tests indicates the environmental extract number we use to track the extracts in our data base. It corresponds to the extract_number_field_based in the metadata and data folder. The negative extraction control with the strongest "band" was placed right to the eDNA extract on each image (labelled hand written with NC x.y).
metadata\:
File containing overview of site names and extract number (field-based or lab-based extraction). The extract_number_field_based corresponds to the identically called column in CRISPR_field_based_classifications.csv file, as the extract_number_lab_based to the column in the file CRISPR_lab_based_classifications.csv file and the qPCR_Cp_2nd_derivative.csv file. The file includes the GPS coordinates of the sampling location (transect start point).
data\:
Folder containing the files with Cp values (qPCR) and the CRISPR-Dx classifications. CRISPR_field_based_classifications.csv file contains the classifications per pool per extract (0: no detection, 1: detection) for the African manatee (Trichechus senegalensis). CRISPR_lab_based_classifications.csv file contains the classifications per pool per extract (0: no detection, 1: detection). qPCR_Cp_2nd_derivative.csv file contains the Cp value of the 8 replicates of each extract.