The devil is in the details: Problems in DNA barcoding practices indicated by systematic evaluation of insect barcodes

Abstract

In recent years, DNA barcoding has rapidly developed as a powerful tool in taxonomy, demonstrating its value in species identification and discovery of cryptic diversity. The number of barcoding sequences of various species continues to grow in the GenBank and BOLD databases; however, the accuracy of sequences and related raw information in public repositories is often questionable. In the present study, based on a dataset of 68,089 Hemiptera COI barcode sequences covering 3,064 species, 1,072 genera, and 48 families, we analyzed genetic differences within and between species and evaluated possible data errors in the insect barcodes. The results showed that errors in the barcode data are not rare, and most of them are due to human errors, such as specimen misidentification, sample confusion, and contamination. A significant portion of these errors can be attributed to inappropriate and imprecise practices in the DNA barcoding workflow. Herein, suggestions are provided to improve the practical operations and workflow of DNA barcoding to reduce human errors.

The Diversity of Parasitoids and Their Role in the Control of the Siberian Moth, Dendrolimus sibiricus (Lepidoptera: Lasiocampidae), a Major Coniferous Pest in Northern Asia

“…This, in turn, contributes to the enhancement of existing genetic databases, facilitating more rapid and precise species identification [100,101]. Furthermore, it aids in the identification of misclassified cases in BOLD and/or NCBI [102,103].…”

Mitochondrial DNA evidence reflects high genetic divergence of Amynthas aspergillum (Oligochaeta: Megascolecidae) in southern China

“…For species with deep intraspecific divergence, inadequate sampling, incomplete lineage sorting and gene flow may lead to incorrect species delimitation (Lin et al., 2021). Therefore, the final species delimitation requires further comprehensive validation from both morphological and molecular aspects, or even in combination of other types of information such as geography, behavior, and ecological preferences (Cheng et al., 2023).…”

“…For species with deep intraspecific divergence, inadequate sampling, incomplete lineage sorting and gene flow may lead to incorrect species delimitation (Lin et al, 2021). Therefore, the final species delimitation requires further comprehensive validation from both morphological and molecular aspects, or even in combination of other types of information such as geography, behavior, and ecological preferences (Cheng et al, 2023). The ancestral area of the clades ranged from E to G and finally to H, indicating that A. aspergillum gradually dispersed toward the east after its origin in Guangxi, and that the Yunnan-Guizhou Plateau, Nanling, and Wuyi Mountains might be the geographical obstacles for its spread to the west and north.…”

Incursion Preparedness, Citizen Science and Early Detection of Invasive Insects: The Case of Aleurocanthus spiniferus (Hemiptera, Aleyrodidae) in France

“…The number of specialists must therefore be maintained, and the discipline must remain alive in the academic world, if we want to maintain these skills. Since the initial identification of the sequenced specimen is correct, DNA barcoding is an efficient way to assign unidentified specimens to known species but the number of errors should not be underestimated [28,29]. Deep learning technologies constitute interesting ways to implement automatic species recognition from pictures [30].…”