DOI: 10.5061/dryad.gb5mkkwzf
title: Environmental DNA data of aquatic insects for habitat suitability models

description: The rapid loss of biodiversity in freshwater systems asks for a robust and
 spatially explicit understanding of species’ occurrences. As two
 complementing approaches, habitat suitability models provide information
 about species’ potential occurrence, while environmental DNA (eDNA) based
 assessments provide indication of species’ actual occurrence.
 Individually, both approaches are used in ecological studies to
 characterize biodiversity, yet they are rarely combined. Here, we
 integrated high-resolution habitat suitability models with eDNA-based
 assessments of aquatic invertebrates in riverine networks to understand
 their individual and combined capacity to inform on species’ occurrence.
 We used eDNA sampling data from 172 river sites and combined the detection
 of taxa from three insect orders (Ephemeroptera, Plecoptera, Trichoptera;
 hereafter EPT) with suitable habitat predictions at a subcatchment level
 (2 km2). Overall, we find congruence of habitat suitability and eDNA-based
 detections. Yet, the models predicted suitable habitats beyond the
 observed number of detections by eDNA sampling, congruent with the
 suitable niche being larger than the realized niche. For local mismatches,
 where eDNA detected a species but the habitat was not predicted suitable,
 we calculated the minimal distance to upstream suitable habitat patches,
 indicating possible sources of eDNA signals from upstream sites
 subsequently being transported along the water flow. We estimated a median
 distance of 1.06 km (range 0.2–42) of DNA transport based on upstream
 habitat suitability, and this distance was significantly smaller than
 expected by null model predictions. This estimated transport distance is
 in the range of previously reported values and allows extrapolations of
 transport distances across many taxa and riverine systems. Together, the
 combination of eDNA and habitat suitability models allows larger scale and
 spatially integrative inferences about biodiversity, ultimately needed for
 the management and protection of biodiversity.
description: # Environmental DNA data of aquatic insects for habitat suitability model
 This dataset belongs to the article: Habitat suitability models reveal the
 spatial signal of environmental DNA in riverine networks submitted by:
 Jeanine Brantschen,
 [jea.brantschen@gmail.com](mailto:jea.brantschen@gmail.com) ## Description
 of the Data and file structure The folder contains the raw data of two
 eDNA sampling campaign across all of Switzerland. For these campaigns, as
 part of the NAWA surface water monitoring by the Federal Office of the
 Environment, eDNA metabarcoding was performed using two different primer
 pairs targeting the COI genetic barcode. This study focused on 127 insect
 species and their distribution patterns based on the two sampling
 campaigns. The pattern from the field eDNA campaign was then compared to
 state-of-the-art SDMs built by a pipeline from another article (cited as
 Adde et al., 2023 in the paper). All data associated with the SDM can be
 found in the related article and will not be included in this repository,
 as it is already publicly available. The sequencing data were generated in
 one paired-end run on an Illumina MiSeq at the GDC, ETH Zurich. The files
 are in FASTA format (R1 being the forward and R2 being the reverse read)
 and can be opened using a text editor or directly fed into a bioinformatic
 pipeline. Additionally, there is another file
 (MS4*Supplements*_IndividualSpecies) showing the 1:1 comparison of the
 individual 127 species based on eDNA and the SDMs. This file is referred
 to in the text as Supplementary 2. **Explanation of data files:**  *
 p677_JB_Leese_201019_MapFile.txt is the metadata file required to
 associate the read samples with environmental parameters. For each sample,
 there is a row providing information about the sampling site. This can be
 read into R to build a phyloseq object. Here is a list of the columns and
 their explanation:  * SampleID: This is the unique name of the sample.  *
 identity: controls( negative/blank), positive control (known composition),
 sample (eDNA sample)  * bank: left or right river bank * site: sampling
 site * canton: geographical unit * filter: replicate 1-4 from one site *
 catchment: river catchment based on swiss topo * BarcodeSequence i5:
 unique barcode sequence forward direction  * BarcodeSequence i7: unique
 barcode sequence reverse direction  * LinkerSequenceForward: Linker
 sequence in the amplicon between barcode and fragment forward direction *
 PrimerSequenceForward: sequencing primer sequence in the amplicon between
 barcode and fragment forward direction * LinkerSequenceReverse: Linker
 sequence in the amplicon between barcode and fragment reverse direction *
 PrimerSequenceForward: sequencing primer sequence in the amplicon between
 barcode and fragment reverse direction * Experiment: sequencing run
 identification * Platform: sequencing platform * Cyclekite: illumination
 chemistry * RunDate: date of the sequencing run  * I5_Index_ID index:
 Nextera index kit number and sequence forward * I7_Index_ID index: Nextera
 index kit number and sequence reverse * PCR_plate: Which PCR plate (1-4)
 this sample was on * PCR_position: Which well position this sample was in
 (1-96 per plate) * description: customizer identifier of the data set and
 run - p677_run201020_COI_ZOTU_Count*Sintax.txt is the processed OTU* table
 including a taxonomic assignment using Syntax. The table contains samples
 as columns and rows as ESVs.  * The rows are the bioinformatically
 generated Exact sequence variances (ESV) for the 12S Mifish barcode. The
 first column (#OTU ID) contains the name of the ESVs, the following
 columns link to the SampleID in the previous file and contain the
 abundance data of the ESVs in a sample. At the end of the table (column
 consensus lineage) is a taxonomic assignment from the phylum to the
 species level.  - p677_run200221_COI_ZOTU_Count_Sintax_ReferenceG.txt is a
 copy of the processed OTU table using a customized reference database to
 improve annotation.  * The rows are the bioinformatically generated Exact
 sequence variances (ESV) for the 12S Mifish barcode. The first column
 (#OTU ID) contains the name of the ESVs, the following columns link to the
 SampleID in the previous file and contain the abundance data of the ESVs
 in a sample. At the end of the table (column consensus lineage) is a
 taxonomic assignment from the phylum to the species level based on the
 curated database (Reference G).  *
 arthropodes_species_matrix_jeanine_2022_12_16_1.5.rds gives the species
 matrix from the species distribution modeling used as raw input.  * This
 file is the species-site-abundance matrix for the insect larvae species,
 the structure is similar to the previous to files, with the latin names of
 aquatic insect species aligned with the catchments of rivers in
 Switzerland based on SwissTopo. This is the output of the habitat
 suitability models. The numeric values indicate the probability of a
 species occurring in a catchment.  -
 MS4_Supplement_IndividualSpecies_copy.pdf is a list of species detected
 with either method.  * This file gives a list of the observed species in
 the orders Ephemeroptera, Trichoptera and Plectopetra and the columns are
 the different methods. This table helps to show which method detected
 which species.  ## Sharing/access Information The sequencing data is only
 publicly available on Dryad as well as additional supplementary files. For
 further information on the R Code or the raw data, please contact the
 corresponding author
 ([jea.brantschen@gmail.com](mailto:jea.brantschen@gmail.com)).