Assessing the effectiveness of DNA barcoding in shark identification.

The conservation status of shark populations has become increasingly concerning, with many species at risk of extinction, largely due to the shark fin trade. Effective conservation and regulation of illegal shark fin trading require accurate identification of shark species from samples. However, traditional DNA barcoding techniques have shown certain limitations during their application. To overcome these issues, this study systematically analyzed shark cytochrome c oxidase subunit I (COI) gene sequences, focusing on the distribution of genetic distances among shark populations and the investigation of DNA barcode gaps at the species level. Our results revealed that the current public shark COI dataset contains inaccuracies, including mislabeled barcodes and species misidentifications. In response, a curated and high-quality reference database for shark species identification was established. Analysis of genetic divergence showed considerable variation in both intraspecific and interspecific distances was observed across different sharks, with 149 out of 353 species displaying clear barcode gaps. Identification thresholds were also found to vary among species. Additionally, twelve COI primer pairs were evaluated, with those developed by Inoue et al. showing superior performance on degraded samples. Application of COI barcoding to 258 shark fin specimens successfully identified the majority of samples, although it failed to discriminate among four closely related species. In contrast, 16S rRNA markers improved resolution, and instances of COI misidentification were attributed to errors within the database. Notably, a significant data imbalance remains, with 56 shark species represented by only a single COI sequence and 208 species lack any reliable reference barcodes. This study not only curated and established a comprehensive DNA barcode library for shark species identification but also evaluated the effectiveness of various primers, offering a valuable framework to standardize species identification procedures.