DNA Barcode Reference Library and Undetected Diversity of Fish Species in the Yuanjiang River, China

The Yuanjiang River, located in the upper reaches of the Red River, constitutes a critical part of the Mountains of Southwest China biodiversity hotspot, which supports a high diversity of fish species. Nevertheless, relatively systematic researches of fish diversity aiming at the Yuanjiang River are rare, scattered and outdated. In our study, we yielded 764 DNA barcodes belonging to 64 fish species to evaluate fish diversity in the Yuanjiang River. Barcoding gap analysis and DNA-based delimitation obtained high identification success rate (> 93%), indicating DNA barcoding is an efficient approach to delimit fish in the Yuanjiang River. However, four species were characterized by deep intraspecific divergences, generating multiple clades and/or Molecular Operational Taxonomic Units (MOTUs), suggesting these species might own undetected species. Meanwhile, two closely related species within genus Schistura, i.e. S. calichromus and S. caudofurca, were failed to delimited by DNA barcoding technique, which was indicative of recent speciation. In sum, this study built a reliable DNA barcode reference library for fish species in the Yuanjiang River and unveiled hidden fish diversity.