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Decision‐making and best practices for taxonomy‐free environmental DNA metabarcoding in biomonitoring using Hill numbers


Mächler, Elvira; Walser, Jean‐Claude; Altermatt, Florian (2021). Decision‐making and best practices for taxonomy‐free environmental DNA metabarcoding in biomonitoring using Hill numbers. Molecular Ecology, 30(13):3326-3339.

Abstract

Environmental DNA (eDNA) metabarcoding is raising expectations for biomonitoring of organisms that have hitherto been neglected. To bypass current limitations in taxonomic assignments due to incomplete or erroneous reference databases, taxonomy-free approaches are proposed for biomonitoring at the level of operational taxonomic units (OTUs). This is challenging, because OTUs cannot be annotated and directly compared against classically derived taxonomic data. The application of good stringency treatments to infer the validity of OTUs and clear understanding of the consequences of such treatments is especially relevant for biodiversity assessments. We investigated how common practices of stringency filtering affect eDNA diversity estimates in the statistical framework of Hill numbers. We collected water eDNA samples at 61 sites across a 740-km2 river catchment, reflecting a spatially realistic scenario in biomonitoring. After bioinformatic processing of the data, we studied how different stringency treatments affect conclusions with respect to biodiversity at the catchment and site levels. The applied stringency treatments were based on the consistent appearance of OTUs across filter replicates, a relative abundance cut-off and rarefaction. We detected large differences in diversity estimates when accounting for presence/absence only, such that detected diversity at the catchment scale differed by an order of magnitude between the treatments. These differences disappeared when using stringency treatments with increasing weighting of the OTU abundances. Our study demonstrated the usefulness of Hill numbers for biodiversity analyses and comparisons of eDNA data sets that strongly differ in diversity. We recommend best practice for data stringency filtering for biomonitoring using eDNA.

Abstract

Environmental DNA (eDNA) metabarcoding is raising expectations for biomonitoring of organisms that have hitherto been neglected. To bypass current limitations in taxonomic assignments due to incomplete or erroneous reference databases, taxonomy-free approaches are proposed for biomonitoring at the level of operational taxonomic units (OTUs). This is challenging, because OTUs cannot be annotated and directly compared against classically derived taxonomic data. The application of good stringency treatments to infer the validity of OTUs and clear understanding of the consequences of such treatments is especially relevant for biodiversity assessments. We investigated how common practices of stringency filtering affect eDNA diversity estimates in the statistical framework of Hill numbers. We collected water eDNA samples at 61 sites across a 740-km2 river catchment, reflecting a spatially realistic scenario in biomonitoring. After bioinformatic processing of the data, we studied how different stringency treatments affect conclusions with respect to biodiversity at the catchment and site levels. The applied stringency treatments were based on the consistent appearance of OTUs across filter replicates, a relative abundance cut-off and rarefaction. We detected large differences in diversity estimates when accounting for presence/absence only, such that detected diversity at the catchment scale differed by an order of magnitude between the treatments. These differences disappeared when using stringency treatments with increasing weighting of the OTU abundances. Our study demonstrated the usefulness of Hill numbers for biodiversity analyses and comparisons of eDNA data sets that strongly differ in diversity. We recommend best practice for data stringency filtering for biomonitoring using eDNA.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Institute of Evolutionary Biology and Environmental Studies
08 Research Priority Programs > Global Change and Biodiversity
Dewey Decimal Classification:570 Life sciences; biology
Scopus Subject Areas:Life Sciences > Ecology, Evolution, Behavior and Systematics
Life Sciences > Genetics
Uncontrolled Keywords:Genetics, Ecology, Evolution, Behavior and Systematics
Language:English
Date:1 July 2021
Deposited On:24 Feb 2022 10:09
Last Modified:28 Jan 2024 02:45
Publisher:Wiley-Blackwell Publishing, Inc.
ISSN:0962-1083
Additional Information:This is the peer reviewed version of the following article: Mol Ecol, 2021 Jul;30(13):3326-3339, which has been published in final form at https://doi.org/10.1111/mec.15725. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. (http://www.wileyauthors.com/self-archiving)
OA Status:Green
Publisher DOI:https://doi.org/10.1111/mec.15725
PubMed ID:33188644
Project Information:
  • : FunderFP7
  • : Grant ID200999
  • : Project TitleSTOPLATENT-TB - LATENT TUBERCULOSIS: New tools for the detection and clearance of dormant Mycobacterium tuberculosis.
  • : FunderSNSF
  • : Grant ID31003A_173074
  • : Project TitleRiverDNA: uncovering fundamental biodiversity in riverine systems using environmental DNA
  • : FunderSNSF
  • : Grant IDPP00P3_179089
  • : Project TitleBridging biodiversity and ecosystem functioning: a meta-ecosystem perspective
  • Content: Accepted Version