Assessment of fish diversity in the South China Sea using DNA taxonomy

The South China Sea (SCS) is part of the Indo-West Pacific Ocean, which is regarded as harboring a high diversity of fish. However, our knowledge of true fish diversity especially among pelagic and deep-sea families is still insufficient. Here, we used DNA barcoding and DNA identification to investigate the fish diversity and distribution in the three most important fisheries regions in the South China Sea, Xisha Islands (Paracel Islands), Dongsha Islands (Pratas Islands) and Nansha Islands (Spratly Islands). We identified a total of 109 species in our samples based on morphological characterization, yet 307 DNA barcodes using the 602 base-pair fragments of the COI gene suggested 116 putative species by one of DNA taxonomic approaches (GMYC). The intraspecific divergences (K2P pairwise distances) averaged 0.25 % (ranged 0 - 0.89 %), while congeneric divergences averaged 4.56 %, (ranged 1.18 %–9.56 %). The results suggest that COI-based barcoding can be effectively used for marine fish identification in the South China Sea and that it allows a realistic idea of diversity and management of fishery resources.