The Application of DNA Barcoding in Crustacean Larvae Identification from the Zhongsha Islands, South China Sea

Abstract

Marine crustaceans are known as a group with high morphological diversity and great economic value. Most species have planktonic larval stages that are difficult to identify to species level using traditional approaches because of insufficient morphological diagnostic characters or taxonomic descriptions. We used DNA barcoding and molecular species identification to investigate the species diversity and distribution of crustacean larvae in the Zhongsha Islands waters, South China Sea. In total, 108 sequences were obtained from crustacean larvae collected in the Zhongsha Islands waters in 2019 using vertical hauls between the depths of 5 and 200 m. The molecular classification approach confirmed that 108 sequences represented crustaceans typical to the South China Sea, with 70 species identified, representing 43 genera, 23 families, and 4 orders. However, the cytochrome c oxidase subunit I gene sequences of only 27 species identified from the larval samples matched with available sequences taken from adults in GenBank. The comparison of K2P distances yielded a notable gap of 3.5–10.7% between intraspecific and interspecific distances across the sequence dataset. More than 80% of the crustacean larvae species belonged to the order Decapoda, and they displayed marked differences in their distributionsin the Zhongshan Islands waters. The orders Calanoida and Amphipoda were represented by the fewest species, which were recorded only at the edge of the Zhongsha Atoll.

DNA barcoding of marine fish species in the waters surrounding Hainan Island, northern South China Sea

“…When utilizing the COI gene as a DNA barcode for animal species, the intraspecific Kimura 2-parameter (K2P) distances typically fall below 1% and seldom exceed 2% (Hebert et al, 2003). However, it is worth noting that certain arthropod groups, such as crustaceans, may exhibit comparatively higher distances (Costa et al, 2007;Xu et al, 2022). In our fish dataset, the average intraspecific Kimura 2-parameter (K2P) pairwise distance was calculated to be 0.15%, with a range spanning from 0% to 0.78%.…”

“…These tools provided complementary perspectives on species boundaries, allowing us to make more informed inferences based on the COI dataset. For detailed examination techniques and parameter configurations, we kindly refer the reader to our antecedently issued publications (Xu et al, 2019;Xu et al, 2022). The divergence of COI sequences was calculated using the Kimura 2-parameter (K2P) distance model in MEGA version 6 (Kumar et al, 2008;Tamura et al, 2013).…”

“…This remarkable feature enables the identification of organisms during their larval stage, even in the absence of distinct morphological characteristics. By comparing the sequences of unidentified larval specimens with those of previously documented adults stored in the reference sequence library, it becomes possible to accurately determine their identities (Barber and Boyce, 2006;Caterino and Tishechkin, 2006;Kusbiyanto et al, 2020;Huang et al, 2022;Xu et al, 2022). These endeavors have made substantial contributions to the detection of previously unknown species and accelerated the identification of sibling species or cryptic species.…”