Commercially important hairtails, Trichiurus spp., are widely distributed throughout China’s marine waters. Because eggs of these species are difficult to identify and the taxonomy of the group has recently been resolved, their spawning grounds in the northern South China Sea (SCS) are not well known. We identified three Trichiurus species (T. japonicus, T. nanhaiensis, and T. brevis) using DNA barcodes in spring and late summer–autumn ichthyoplankton surveys of 2019 in the northern SCS. Egg distributions reveal that the spawning grounds of T. japonicus and T. nanhaiensis occur mainly from the central and southern Beibu Gulf, along Hainan Island, to the waters off the Pearl River Estuary, and that egg densities are higher in spring than in late summer-autumn. Spawning of T. japonicus commonly occurs along the continental shelf, T. nanhaiensis along the continental shelf to slope (over seabed depths of 42–380 m), and T. brevis mainly in shallow water. Considering the salinity and temperature data, we found that the eggs of Trichiurus were associated with specific water masses. In spring, eggs of T. japonicus and T. nanhaiensis occurred at central and southern Beibu Gulf water mass (CSBGWM) and South China Sea surface water mass (SCSWM). While in late summer-autumn, eggs of T. japonicus and T. nanhaiensis mainly occurred in the waters of SCSWM. Our findings reveal that the occurrence of Trichiurus eggs and their spatial and temporal distribution are determined by hydrological conditions.

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Ichthyoplankton assemblages and their relationship with environmental variables are investigated in waters off the Pearl River Estuary in spring and autumn of 2019. Of 80 ichthyoplankton taxa identified using DNA barcode and morphological methods, 61 are identified to species. The most abundance families (Carangidae, Trichiuridae, Mullidae, and Scombridae) account for 61.34% of the horizontal total catch in spring, while Menidae and Carangidae are the most abundant families identified in autumn, accounting for 89.72% of the horizontal total catch. Cluster analysis identifies three species assemblages in spring, and four in autumn based on horizontal trawls. Relationships between assemblage structure and environmental variables (in situ and remote sensed) are determined by canonical correspondence analysis. Ichthyoplankton assemblage structure appears to be strongly influenced by sea level anomalies, salinity, water depth, temperature at 10 m depth, and distance from shore. We demonstrate the efficacy of using DNA barcode to identify ichthyoplankton, and suggest how these data can be used to protect fish spawning grounds in waters off the Pearl River Estuary.

Delimiting ichthyoplankton is fundamental work for monitoring the recruitment process and identifying the spawning and nursing grounds of fishes. Nevertheless, it is extremely difficult to identify the fish during the early stages at the species level based on morphological characters because of the paucity of diagnostic features. In this study, we investigated the fish larval community through large-scale ecosystemic sampling in South China Sea (SCS) during 2013 and 2017 using DNA barcodes. To maintain the morphologies of fish larvae, we preserved the larvae in formalin and developed a technique to recover their DNA. Among the 3,500 chosen larvae, we successfully extracted DNA from 2,787 larval samples and obtained 1,006 high-quality sequences. Blast searches showed that 408 larvae (i.e., 40.5%) could be unambiguously identified to species, 413 larvae (i.e., 41.1%) were ambiguously species delimitation, and 185 larvae (i.e., 18.4%) showed a low match similarity with target sequences. A total of 101 species were identified, among which 38 and 33 species corresponded to demersal and reef-associated species, whereas the remaining 30 species corresponded to benthopelagic, pelagic-oceanic, bathypelagic, and pelagic-neritic species. High-quality larval photographs of the 101 diagnosed species showed intact morphological characters and thus provided a reference for identifying fish species during the early stages based on morphological characters. Our study highlighted the possibility of recovering and amplifying DNA from formalin-fixed samples and provided new insight into the fish larval community in the SCS.

The Beibu Gulf in China is rich in fish resources. However, only a small number of commercially developed fish stocks have been specifically assessed owing to limited data and expertise. In this study, 19 perciform fish populations in the Beibu Gulf were assessed using a length-based Bayesian biomass (LBB) estimator method, which is a new approach to evaluate a fishery’s status using length frequency (LF) data. The results showed that only 21% of the evaluated stocks were healthy and 79% were overfished. In particular, 26 and 21% of the assessed species had collapsed and were grossly overfished, respectively. Only 11 and 21% of the assessed species were slightly overfished and overfished, respectively. The ratios between the mean and optimum length (Lmean/Lopt) and between the mean length at first capture and the mean length, which maximizes catch and biomass (Lc/Lc_opt), were below one in 14 out of the 19 stocks, suggesting a truncated length structure and fishing of undersized individuals. The ratio of the 95th percentile length to asymptotic length L95th/Linf was close to one (>0.9) in 10 of 19 stocks, suggesting that at least some large fish were still present. Our research confirmed that the fishery resources in the Beibu Gulf were seriously overfished and provided evidence that LBB was an efficient method to evaluate the fishery resources. Fishery managers need to take specific measures to restore fishery resources.