DOI: 10.5061/dryad.v41ns1s61
title: Comparing eDNA and transect methods for aquatic biodiversity assessment in lakes and ponds

description: Biodiversity monitoring increasingly relies on molecular methods such as
 eDNA metabarcoding. However, sound applications have so far been only
 established for a limited number of taxonomic groups. More information on
 the strengths and weaknesses of eDNA methods, especially for poorly
 covered groups, is essential for practical applications to achieve the
 highest possible reliability. We compared amphibian and Odonata
 data from eDNA metabarcoding and traditional transect walks on N=56 plots
 in 38 water bodies distributed over six extraction sites for building
 materials in Northwest Germany. The traditional amphibian assessment
 included visual encounters, dip netting and acoustic detection, while
 Odonata were assessed through exuviae. In total, both methods
 detected eight out of eleven amphibian species, while the remaining three
 species were detected by eDNA only. We did not find differences in
 amphibian species numbers per plot, but mean detection probabilities were
 higher with metabarcoding. In contrast, both methods detected 10 out of 29
 Odonata species, while the remaining 19 species were detected by exuviae
 only. Species numbers per plot were higher for exuviae and only 30% of
 species were detected with metabarcoding. The species identified by eDNA
 were those with high abundance and their detection probabilities were
 similar to transect walks. The results for amphibians show equal
 suitability and high complementarity of the compared methods.
 Metabarcoding detected species more efficiently and therefore offers a
 suitable protocol for biodiversity monitoring. For Odonata, eDNA
 metabarcoding showed considerable gaps, implying the need for protocol
 evaluation and improvement in assessment of ecological communities based
 on eDNA.
description: # Comparing eDNA and transect methods for aquatic biodiversity assessment
 in lakes and ponds
 [https://doi.org/10.5061/dryad.v41ns1s61](https://doi.org/10.5061/dryad.v41ns1s61) ## Description of the data and file structure Raw data for Amphibian and Odonata diversity from ponds and lakes in mining sites around Germany. Data collected via transect walks and eDNA metabarcoding in 2022. ### Files and variables **Data:** xlsx-files include notes describing all variables and NA values #### File: raw\_data\_amphibians\_eDNA\_and\_transects.xlsx #### File: raw\_data\_Odonata\_eDNA\_and\_transects.xlsx #### File: metadata\_publication.xlsx **R-Scripts:** Scripts include the complete data analysis for "Comparing eDNA and transect methods for aquatic biodiversity assessment in lakes and ponds". "Schwesig_et_al_2024_-Data_analysis.R" contains the analyses for five sampling runs of transect walks and two sampling events for eDNA while "Schwesig_et_al_2024-Data_analysis-_reduced_dataset.R" contains the results included in the supplementary material with the reduced data set for the two runs where eDNA sampling took place. #### File: Schwesig\_et\_al\_2024\_-\_Data\_analysis.R #### File: Schwesig\_et\_al\_2024\_-Data\_analysis-\_reduced\_dataset.R ## Access information Further related data can be found at the European Nucleotide Archive (Accession number [PRJEB73319](https://www.ebi.ac.uk/ena/browser/view/PRJEB73319)) and on figshare ([https://doi.org/10.6084/m9.figshare.26067520.v1](https://doi.org/10.6084/m9.figshare.26067520.v1)).