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Dryad

Using eDNA for monitoring fish and invertebrate biodiversity in freshwater ecosystems

Cite this dataset

James, Joanna et al. (2024). Using eDNA for monitoring fish and invertebrate biodiversity in freshwater ecosystems [Dataset]. Dryad. https://doi.org/10.5061/dryad.1c59zw44f

Abstract

Global biodiversity is facing an extinction crisis leading to increasing pressure on industries to monitor their potential environmental impact. Relatedly, there is demand for more efficient biodiversity monitoring methods, resulting in growing interest in the use of environmental DNA (eDNA). Many questions, however, regarding the reliability of this relatively novel method remain, particularly for non-specialist end-users of the technology.

Here, the use of commercially available (in the UK) eDNA assays for monitoring freshwater fish and invertebrate biodiversity was compared to conventional surveillance techniques. Samples were collected from different habitats, on varying spatial scales and using multiple sampling regimes to assess how eDNA results were affected.

For aquatic macroinvertebrates and fish, more taxa were detected by eDNA than conventional surveys conducted in parallel, and for fish, all taxa detected by conventional monitoring were confirmed by eDNA.

For aquatic macroinvertebrates, several species were only detected through conventional methods, and the number of families detected by eDNA was lower than for conventional monitoring at all sites.

eDNA results varied significantly between sampling locations within lentic sites and, for lotic sites, with the number of subsamples collected.

In terms of  practical implications, this study demonstrates the need for bespoke sampling protocols when collecting eDNA samples. This study improves understanding of using eDNA for detecting aquatic taxa that could inform species surveillance protocols. These are essential if eDNA is to be used by practitioners as a regulatory monitoring tool.

README: Using eDNA for monitoring fish and invertebrate biodiversity in freshwater ecosystems

https://doi.org/10.5061/dryad.1c59zw44f

The use of commercially available (in the UK) eDNA assays for monitoring freshwater fish and invertebrate biodiversity was compared to conventional surveillance techniques (electro-fishing and kick-netting respectively). Samples were collected from different freshwater habitats, on varying spatial scales and using multiple sampling regimes to assess how eDNA results were affected. This data set provides the raw data used to carry out these investigations. All eDNA analyses were conducted by a reputable UK based provider and conventional surveys conducted by suitably experienced freshwater water ecologists within UK based consultancies. 

Description of the data and file structure

The data set is split into a series of tab relating to the different research questions being investigated as follows:

Tab 1 Lentic eDNA - provides details of the total number of invertebrate taxa detected using metabarcoding at each reservoir surveyed. Details are also provided on the site number within each reservoir and the number of sub-samples collected. 

Tab 2 Lotic eDNA - provides details of the total number of invertebrate and fish taxa detected using metabarcoding at each river surveyed. Details are also provided on the site number within each river and the number of sub-samples collected. 

Tab 3 Lotic eDNA vs Conventional - provides details of the number of invertebrate and fish taxa detected using metabarcoding and conventional monitoring conducted in tandem at each river surveyed. Details are also provided on the number of taxa detected by eDNA but not conventional methods and vice versa. Further details on the taxa detected in each of these samples is provided in the following tabs (more details below).

Tab 4 Fish eDNA Win. Clough - provides details of the taxa detected at Windeldon Clough using metabarcoding. 

Tab 5 Fish eDNA Breary Banks - provides details of the taxa detected at Breary Banks using metabarcoding. 

Tab 6 Fish eDNA Booth D Clough - provides details of the taxa detected at Booth Dean Clough using metabarcoding. 

Tab 7 Fish Convent. Win. Clough - provides details of the taxa detected at Windeldon Clough using electro-fishing. 

Tab 8 Fish Convent. Breary Banks - provides details of the taxa detected at Breary Banks using electro-fishing. 

Tab 9 Fish Convent. Booth D Clough - provides details of the taxa detected at Booth Dean Clough using electro-fishing. 

Tab 10 Invert. eDNA Win. Clough - provides details of the taxa detected at Windeldon Clough using metabarcoding. N/A indicates that identification to this taxonomic level was not possible. 

Tab 11 Invert. eDNA Breary Banks - provides details of the taxa detected at Breary Banks using metabarcoding. N/A indicates that identification to this taxonomic level was not possible. 

Tab 12 Invert. eDNA Booth D Clough - provides details of the taxa detected at Booth Dean Clough using metabarcoding. N/A indicates that identification to this taxonomic level was not possible. 

Tab 13 Invert. Convent. Win. Clough - provides details of the taxa detected at Windeldon Clough using kick-netting. 

Tab 14 Invert. Convent. Breary Banks - provides details of the taxa detected at Breary Banks using kick-netting. 

Tab 15 Invert. Convent. Booth D Clough - provides details of the taxa detected at Booth Dean Clough using kick-netting.

Funding

Yorkshire Water