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Sharpening the DNA barcoding tool through a posteriori taxonomic validation: The case of Longitarsus flea beetles (Coleoptera: Chrysomelidae)
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Sharpening the DNA barcoding tool through a posteriori taxonomic validation: The case of Longitarsus flea beetles (Coleoptera: Chrysomelidae)
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Sharpening the DNA barcoding tool through a posteriori taxonomic validation: The case of Longitarsus flea beetles (Coleoptera: Chrysomelidae)
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Journal Article
Sharpening the DNA barcoding tool through a posteriori taxonomic validation: The case of Longitarsus flea beetles (Coleoptera: Chrysomelidae)
2020
Overview
The accuracy of the DNA barcoding tool depends on the existence of a comprehensive archived library of sequences reliably determined at species level by expert taxonomists. However, misidentifications are not infrequent, especially following large-scale DNA barcoding campaigns on diverse and taxonomically complex groups. In this study we used the species-rich flea beetle genus Longitarsus, that requires a high level of expertise for morphological species identification, as a case study to assess the accuracy of the DNA barcoding tool following several optimization procedures. We built a cox1 reference database of 1502 sequences representing 78 Longitarsus species, among which 117 sequences (32 species) were newly generated using a non-invasive DNA extraction method that allows keeping reference voucher specimens. Within this dataset we identified 69 taxonomic inconsistencies using barcoding gap analysis and tree topology methods. Threshold optimisation and a posteriori taxonomic revision based on newly generated reference sequences and metadata allowed resolving 44 sequences with ambiguous and incorrect identification and provided a significant improvement of the DNA barcoding accuracy and identification efficacy. Unresolved taxonomic uncertainties, due to overlapping intra- and inter-specific levels of divergences, mainly regards the Longitarsus pratensis species complex and polyphyletic groups L. melanocephalus, L. nigrofasciatus and L. erro. Such type of errors indicates either poorly established taxonomy or any biological processes that make mtDNA groups poorly predictive of species boundaries (e.g. recent speciation or interspecific hybridisation), thus providing directions for further integrative taxonomic and evolutionary studies. Overall, this study underlines the importance of reference vouchers and high-quality metadata associated to sequences in reference databases and corroborates, once again, the key role of taxonomists in any step of the DNA barcoding pipeline in order to generate and maintain a correct and functional reference library.
Publisher
Public Library of Science,Public Library of Science (PLoS)
Subject
