DOI: 10.5061/dryad.6wwpzgnb8
title: Airborne DNA and spider webs outperform other eDNA sources for monitoring terrestrial vertebrates

description: Understanding the strengths and limitations of different environmental DNA
 substrates is essential for optimizing terrestrial vertebrate surveys and
 monitoring. However, the performance of newly explored substrates
 (airborne eDNA, vegetation swabs, spiderwebs) compared to longstanding
 eDNA sources (water and soil) is uncertain. Using a metabarcoding
 approach, we assessed vertebrate eDNA diversity across seven substrates:
 three airborne DNA collection methods (a powered fan system, and two
 passive collection methods), spider webs, vegetation swabs, water, and
 soil at two sites. The highest species richness was detected by powered
 air samples and spider webs (powered air: 83 at Perth Zoo, 44 at
 Karakamia; spider webs: 62 and 40, respectively), with no significant
 difference in the community composition, suggesting they capture eDNA from
 similar sources however, all substrates contributed unique detections.
 Passive airborne DNA collection, though less efficient than powered
 devices, (mean species richness per sample: 14.8 vs. 5.8 at Perth Zoo; 6.9
 vs. 2.7 at Karakamia), demonstrated great potential as their low cost and
 simplicity may enable increased replication or longer deployment times,
 potentially increasing the probability of species detection. Our direct
 comparison of terrestrial eDNA substrates shows that airborne DNA is a
 step forward and not just hype. However, substrate-specific biases were
 evident, with vegetation swabs favouring arboreal mammals while water was
 dominated by aquatic and semi-aquatic species, highlighting the influence
 of species ecology on DNA deposition. eDNA studies targeting terrestrial
 vertebrates must consider the heterogeneity of vertebrate DNA distribution
 across ecosystems and the need for careful selection of eDNA substrates.
description: # Airborne DNA and spider webs outperform other eDNA sources for
 monitoring terrestrial vertebrates Dataset DOI:
 [10.5061/dryad.6wwpzgnb8](10.5061/dryad.6wwpzgnb8) ## Description of the
 data and file structure Metabarcoding data generated from two assays and
 seven sample types collected: three different methods were used to collect
 eDNA from the air - powered air samplers, wind-powered samplers, and bare
 filter media as a passive collection method and soil, spider webs, swabbed
 vegetation surfaces and water samples. All samples were collected
 throughout both Karakamia Wildlife sanctuary and Perth Zoo. ### Files and
 variables #### File: bc1_16S.txt and bc2_16S.txt **Description:** Text
 file containing the unique ID barcoded tags required to demultiplex raw
 16S Reptile sequences #### File: bc1_12S.txt, bc2_12S.txt, bc3_12S.txt and
 bc4_12S.txt **Description:** Text file containing the unique ID barcoded
 tags required to demultiplex raw 12S-V5 sequences: #### File:
 Substrate_comparison_metadata.csv **Description:** Contains site and
 sample metadata ##### Variables * sample_id: Unique sample identifier  *
 site_id: Unique sample site identifier * Latitude: Sample site latitude *
 Longitude: Sample site longitude * Site: Greater site identifier
 (Karakamia, Perth Zoo) * Habitat: Habitat type * Sample_method: Substrate
 type sampled #### File: NextSeq02_FTP01_S1_R1_001.fastq.gz
 **Description:** compressed sequence file containing raw sequences from
 16S Reptile paired-end illumina NextSeq run #### File:
 NextSeq02_FTP01_S1_R2_001.fastq.gz **Description:** compressed sequence
 file containing raw sequences from 16S Reptile paired-end illumina NextSeq
 run #### File: NSRun03_FTP401_S1_L001_R1_001.fastq.gz
 **Description:** compressed sequence file containing raw sequences from
 12S-V5 single-end illumina NextSeq run #### File:
 eDNAFlow_LCA_results_16S_Reptile.zip **Description:** Filtered data
 produced after sequence analysis using the eDNAFlow bioinformatics
 pipeline and a custom lowest common ancestor (LCA) assignment script for
 the 16S Reptile assay. These data represent the final curated sequence
 outputs used in the associated publication. This folder contains four
 subfolder containing the following files: * **06_Unique_ZOTUs*** – fasta
 files containing zero-radius operational taxonomic units (ZOTUs) generated
 after quality filtering and dereplication and .txt files containing
 associated ZOTU table. * **07_blast*** – Results of BLASTN searches of
 each ZOTU against the local GenBank nucleotide database. * **08_lulu*** –
 curtained_zotuTable.tab containing output after LULU post-clustering
 curation and lulu_zotu_map.tab listing retained and merged ZOTUs with
 similarity and co-occurrence information used to identify redundant OTUs.
 * **09_taxonomyAssigned*** – Final taxonomic assignments produced using
 custom LCA pipeline. #### File: eDNAFlow_LCA_results_12S-V5.zip
 **Description:** Filtered data produced after sequence analysis using the
 eDNAFlow bioinformatics pipeline and a custom lowest common ancestor (LCA)
 assignment script for the 12S-V5 assay. These data represent the final
 curated sequence outputs used in the associated publication. This folder
 contains four subfolder containing the following files: *
 **06_Unique_ZOTUs*** – fasta files containing zero-radius operational
 taxonomic units (ZOTUs) generated after quality filtering and
 dereplication and .txt files containing associated ZOTU table. *
 **07_blast*** – Results of BLASTN searches of each ZOTU against the local
 GenBank nucleotide database. * **08_lulu*** – curated_zotuTable.tab
 containing output after LULU post-clustering curation and
 lulu_zotu_map.tab listing retained and merged ZOTUs with similarity and
 co-occurrence information used to identify redundant OTUs. *
 **09_taxonomyAssigned*** – Final taxonomic assignments produced using
 custom LCA pipeline. #### File: Distance_matrix.csv **Description:** Data
 matrix consisting of both occurrence (presence/absence) and distance to
 eDNA detection from Perth Zoo eDNA samples  ## Access information Data was
 derived from the following sources: * All sequencing data was generated on
 the illumina NextSeq 1000/2000 platform  * All sequencing analysis was
 conducted using eDNAFlow bioinformatics pipeline