Journal Article

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

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

2025

Overview

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 (Nflies legs per pool = 105). The other involved non‐destructively extracting DNA from a large pool of entire flies (Nflies per pool = 105). We tested these methods on flies collected at eight sites, representing three different habitats across five countries in sub‐Saharan Africa (Nflies/site = 105; Nflies 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 (Nflies per pool = 7; Nflies per site = 105 flies). The non‐destructive extraction from large pools of entire flies detected a greater number of mammals (Nspecies detections total = 58; x¯species/site $$ {\\overline{x}}_{\\mathrm{species}/\\mathrm{site}} $$  = 7.3; range = 1–12) than the destructive extraction from large pools of fly legs (Nspecies detections total = 15; x¯species/site $$ {\\overline{x}}_{\\mathrm{species}/\\mathrm{site}} $$  = 1.9; range = 0–3), while detecting a similar number of mammals as the destructive extraction from small pools of entire flies (Nspecies detections total = 67; x¯species/site $$ {\\overline{x}}_{\\mathrm{species}/\\mathrm{site}} $$  = 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. Metabarcoding of invertebrate‐derived DNA (iDNA) is an excellent tool for assessing terrestrial mammal diversity, but the time and costs associated with sample processing constrain its wider adoption. Our study indicates that the non‐destructive extraction of large pools of entire fly bodies has the potential to streamline and reduce the costs of fly iDNA extraction.

• Publisher: John Wiley & Sons, Inc,Wiley
• Subject: Arthropods / Biodiversity / Biomonitoring / bulk pooling / Deoxyribonucleic acid / DNA / DNA barcoding / Ecosystems / environmental DNA / Invertebrates / invertebrate‐derived DNA / Leg / Mammals / non‐destructive DNA extraction / Protocol / Species / terrestrial biomonitoring / Vertebrates