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<p>Accurate species-level identification is crucial for freshwater biomonitoring, especially in the context of the Water Framework Directive. The use of DNA metabarcoding holds potential as an alternative to conventional morphological approaches, yet its reliability depends on the quality and completeness of reference databases. In this study, we assessed the taxonomic coverage and identification accuracy of the Barcode of Life Data System (BOLD) for five aquatic insect orders commonly used as bioindicators: Ephemeroptera, Plecoptera, Trichoptera, Coleoptera, and Diptera. Using reverse taxonomy, we analysed 595 specimens from 27 WFD monitoring sites across Slovakia. The results showed that 94% of the sequences matched 142 existing Barcode Index Numbers (BINs), while 35 sequences formed 22 new BINs, predominantly within Diptera. Over 70% of BINs from mayflies, caddisflies, and aquatic beetles corresponded to a single Linnaean species, but this proportion was moderately lower for dipterans and stoneflies. Overall, 61% of sequences could be reliably assigned to a unique Linnaean species, 33% matched multiple species, and 6% remained unidentified. Identification success varied across insect orders and sites, with mayflies, caddisflies, and aquatic beetles showing consistently high accuracy, reaching a median of over 80% of individuals per site identified to a unique Linnaean species, while Diptera and Plecoptera showed greater variability. A key challenge was BINs linked to multiple species, likely due to misidentification, synonymy, or low COI divergence. Nevertheless, our results underscore the potential of DNA-based biomonitoring and highlight the need for improved taxonomic resolution and rigorous curation of reference databases to ensure satisfactory species-level identification.</p>

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Is the DNA barcode database fit for purpose? Assessing the feasibility of reverse taxonomy in five key aquatic insect orders relevant to freshwater biomonitoring under the Water Framework Directive

  • 期刊论文

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  • 发表日期：

    2025年7月8日

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  • Michaela Šamulková,
  • Zuzana Čiamporová-Zaťovičová,
  • Fedor Čiampor,
  • Kornélia Tuhrinová,
  • Patrik Macko

摘要

Accurate species-level identification is crucial for freshwater biomonitoring, especially in the context of the Water Framework Directive. The use of DNA metabarcoding holds potential as an alternative to conventional morphological approaches, yet its reliability depends on the quality and completeness of reference databases. In this study, we assessed the taxonomic coverage and identification accuracy of the Barcode of Life Data System (BOLD) for five aquatic insect orders commonly used as bioindicators: Ephemeroptera, Plecoptera, Trichoptera, Coleoptera, and Diptera. Using reverse taxonomy, we analysed 595 specimens from 27 WFD monitoring sites across Slovakia. The results showed that 94% of the sequences matched 142 existing Barcode Index Numbers (BINs), while 35 sequences formed 22 new BINs, predominantly within Diptera. Over 70% of BINs from mayflies, caddisflies, and aquatic beetles corresponded to a single Linnaean species, but this proportion was moderately lower for dipterans and stoneflies. Overall, 61% of sequences could be reliably assigned to a unique Linnaean species, 33% matched multiple species, and 6% remained unidentified. Identification success varied across insect orders and sites, with mayflies, caddisflies, and aquatic beetles showing consistently high accuracy, reaching a median of over 80% of individuals per site identified to a unique Linnaean species, while Diptera and Plecoptera showed greater variability. A key challenge was BINs linked to multiple species, likely due to misidentification, synonymy, or low COI divergence. Nevertheless, our results underscore the potential of DNA-based biomonitoring and highlight the need for improved taxonomic resolution and rigorous curation of reference databases to ensure satisfactory species-level identification.