An Exploration of <scp>DNA</scp> Extraction Methods of Fly <scp>iDNA</scp> for Scalable Biodiversity Monitoring

ABSTRACT Metabarcoding of invertebrate‐derived DNA (iDNA) is an excellent tool for assessing terrestrial mammal diversity. A major constraint to wider adoption is the time and costs associated with sample processing. Here, we explored the effectiveness of bulk fly iDNA extraction, which increased the pooling of flies by an order of magnitude over currently used methods. One extraction method involved removing a single leg per fly from many flies, pooling these legs, and destructively extracting DNA from the pool ( N flies legs per pool = 105). The other involved non‐destructively extracting DNA from a large pool of entire flies ( N flies per pool = 105). We tested these methods on flies collected at eight sites, representing three different habitats across five countries in sub‐Saharan Africa ( N flies/site = 105; N flies total = 840). We compared the mammal species detected using metabarcoding of these extracts with extracts generated using an approach that is currently widely used, the cost‐ and labor‐intensive destructive extraction of small pools of entire flies ( N flies per pool = 7; N flies per site = 105 flies). The non‐destructive extraction from large pools of entire flies detected a greater number of mammals ( N species detections total = 58; = 7.3; range = 1–12) than the destructive extraction from large pools of fly legs ( N species detections total = 15; = 1.9; range = 0–3), while detecting a similar number of mammals as the destructive extraction from small pools of entire flies ( N species detections total = 67; = 8.4; range = 5–15). Our findings indicate that the non‐destructive extraction of large pools of entire fly bodies has the potential to streamline and reduce costs of fly iDNA extraction. We hope this will promote the use of fly iDNA in terrestrial biomonitoring efforts.

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Journal
Environmental DNA
Published
2025-10-29
DOI
https://doi.org/10.1002/edn3.70215
Primary Topic
Environmental DNA in Biodiversity Studies
Type
article
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article

An Exploration of DNA Extraction Methods of Fly iDNA for Scalable Biodiversity Monitoring

Erin G. Wessling, Mimi Arandjelovic, Emmanuelle Normand, Joost van Schijndel et al.
Environmental DNA
Environmental DNA in Biodiversity Studies
article

An Exploration of DNA Extraction Methods of Fly iDNA for Scalable Biodiversity Monitoring

Erin G. Wessling, Mimi Arandjelovic, Emmanuelle Normand, Joost van Schijndel, Volker Sommer, Hjalmar S. Kühl, Kevin E. Langergraber, Samuel Angedakin, Sorrel Jones, Mizuki Murai, Sébastien Calvignac‐Spencer, Christina Lynggaard, Katherine Corogenes, Anthony Agbor, Jan F. Gogarten, Paula Dieguez, Kevin Lee, Mueena Jahan, Christophe Boesch, Fabian H. Leendertz, Alix Armero, Simon Krückemeier
article en

Abstract

ABSTRACT Metabarcoding of invertebrate‐derived DNA (iDNA) is an excellent tool for assessing terrestrial mammal diversity. A major constraint to wider adoption is the time and costs associated with sample processing. Here, we explored the effectiveness of bulk fly iDNA extraction, which increased the pooling of flies by an order of magnitude over currently used methods. One extraction method involved removing a single leg per fly from many flies, pooling these legs, and destructively extracting DNA from the pool ( N flies legs per pool = 105). The other involved non‐destructively extracting DNA from a large pool of entire flies ( N flies per pool = 105). We tested these methods on flies collected at eight sites, representing three different habitats across five countries in sub‐Saharan Africa ( N flies/site = 105; N flies total = 840). We compared the mammal species detected using metabarcoding of these extracts with extracts generated using an approach that is currently widely used, the cost‐ and labor‐intensive destructive extraction of small pools of entire flies ( N flies per pool = 7; N flies per site = 105 flies). The non‐destructive extraction from large pools of entire flies detected a greater number of mammals ( N species detections total = 58; = 7.3; range = 1–12) than the destructive extraction from large pools of fly legs ( N species detections total = 15; = 1.9; range = 0–3), while detecting a similar number of mammals as the destructive extraction from small pools of entire flies ( N species detections total = 67; = 8.4; range = 5–15). Our findings indicate that the non‐destructive extraction of large pools of entire fly bodies has the potential to streamline and reduce costs of fly iDNA extraction. We hope this will promote the use of fly iDNA in terrestrial biomonitoring efforts.

Environmental DNAVol. 7(6)
University of Copenhagen (DK), Harvard University (US), University of St Andrews (GB), Robert Koch Institute (DE), Universitätsmedizin Greifswald (DE), German Centre for Integrative Biodiversity Research (DE), German Primate Center (DE), Universität Greifswald (DE), Gashaka Primate Project (NG), Max Planck Institute for Evolutionary Anthropology (DE), Société de Développement des Forêts (CI), Helmholtz Centre for Infection Research (DE), Helmholtz Institute for RNA-based Infection Research (DE), Senckenberg Museum für Naturkunde Görlitz (DE), University College London (GB), Arizona State University (US), Bangladesh Agricultural Research Institute (BD)
Wildlife Conservation Society, Villum Fonden, Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Deutsche Forschungsgemeinschaft, Ministère de l'Enseignement Supérieur et de la Recherche Scientifique, Max-Planck-Gesellschaft, Ministère de l'Enseignement Supérieur et de la Recherche, Robert Koch Institut, National Park Service
Openalex Percentile: Top 70%
Environmental DNA in Biodiversity Studies
DOIOpen Access PDFOpenAlex
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