Data from: Spiderwebs, soil or leaf swabs to detect environmental DNA from terrestrial vertebrates: what is the best substrate ?

ABSTRACT: As human activities drive biodiversity decline, effective biomonitoring is more crucial than ever to track species distribution changes and inform conservation and restoration actions. Environmental DNA (eDNA) metabarcoding has emerged as a promising tool for the simultaneous detection of multiple taxa. However, while substrates play a crucial role in eDNA studies, limited research has compared substrate performance for terrestrial vertebrate detection, leaving a critical gap in empirical knowledge for large-scale application. This study evaluates and compares the effectiveness of three easy-to-collect substrates: soil, leaf swabs and spider webs, for broad terrestrial vertebrate eDNA monitoring. Specifically, we examined taxonomic richness overlaps among substrates, their effects on wild vertebrate detection probabilities and within-sample PCR repeatability. We analyzed 120 samples from the Landes Forest, an intensively managed temperate forest in Western France, and included additional control samples from the Montpellier zoo to validate our detection capabilities. Using metabarcoding with 12S-V5 and 16Smam primers, we identified 63 taxa at the genus or species level. Our findings highlight the advantages of substrates that passively accumulate airborne DNA (leaf swabs and spider webs) over soil, and position spider webs as a suitable choice for maximizing detection probabilities in rapid eDNA surveys, emphasizing their potential for efficient, scalable biomonitoring. Further research is needed to identify factors affecting eDNA detectability from these substrates, aiming to standardize procedures and move from proof-of-concept to broad use by researchers and managers. FILE DESCRIPTION: Sample collection data This CSV file contains the line id for each sample, with WGS coordinates, substrate type and line type. File name: sample_collection_data.csv Information concerning the samples and the negative controls multiplexed in the MiSeq sequencing run This XLSX file contains the Sample_Name, PCR_Replicate_ID, PCR_Replicate_number, Sample_Plate, Sample_Well, I7_Index_ID, index, I5_Index_ID, index2, Sample type, Primer sets, Sequence file name (read 1 fastq file), Sequence file name (read 2 fastq file) for each of the 756 PCR products multiplexed in the Illumina MiSeq run. File name: Information_concerning_the_samples_multiplexed_in_the_MiSeq_sequencing_run.xlsx MiSeq raw sequences of 12Sv5 & 16Smam minibarcodes from the eDNA samples This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for 123 eDNA samples amplified using 12Sv5 & 16Smam primer sets and sequenced in triplicate using the MiSeq platform. The 756 multiplexed PCR products were indexed using both forward and reverse unique dual indexes (UDIs). The list of these 123 multiplexed samples and the negative controls of this sequencing run are provided in the following XLSX file titled: Information concerning the samples multiplexed in the MiSeq sequencing run. File name: MiSeq_Reads_12Sv5_16Smam_eDNA_Run.zip Raw abundance table of 12Sv5 minibarcode from the eDNA samples This TSV file contains the number of reads for each distinct variant and each PCR product of the eDNA samples and controls sequenced in the MiSeq run before data filtering. File name: 12Sv5_eDNA_raw_abundance.tsv Raw abundance table of 16Smam minibarcode from the eDNA samples This TSV file contains the number of reads for each distinct variant and each PCR product of the eDNA samples and controls sequenced in the MiSeq run before data filtering. File name: 16Smam_eDNA_raw_abundance.tsv Filtered abundance table of 12Sv5 minibarcode from the eDNA samples This XLSX file contains the number of reads for each distinct taxa and each PCR product of the eDNA samples sequenced in the MiSeq run after data filtering. File name: 12Sv5_eDNA_raw_abundance.xlsx Filtered abundance table of 16Smam minibarcode from the eDNA samples This XLSX file contains the number of reads for each distinct taxa and each PCR product of the eDNA samples sequenced in the MiSeq run after data filtering. File name: 16Smam_eDNA_filtered_abundance.xlsx Whole script This ZIP file contains the Rcompendium used to generate derived data, figures and statistical analyses. The folder contains every raw data and script required to reproduce results. File name: BERARD_eDNA_substrates.zip