The purpleback flying squid (Ommastrephidae: Sthenoteuthis oualaniensis) is an important species at higher trophic levels of the regional marine ecosystem in the South China Sea (SCS), where it is considered to show the potential for fishery development. Accordingly, under increasing climatic and environmental changes, understanding the nature and importance of various factors that determine the spatial and temporal distribution and abundance of S. oualaniensis in the SCS is of great scientific and socio-economic interest. Using generalized additive model (GAM) methods, we analyzed the relationship between available environmental factors and catch per unit effort (CPUE) data of S. oualaniensis. The body size of S. oualaniensis in the SCS was relatively small (<19.4 cm), with a shorter lifespan than individuals in other seas. The biological characteristics indicate that S. oualaniensis in the SCS showed a positive allometric growth, and could be suitably described by the logistic growth equation. In our study, the sea areas with higher CPUE were mainly distributed at 10°–11° N, with a 27–28 °C sea surface temperature (SST) range, a sea surface height anomaly (SSHA) of −0.05–0.05 m, and chlorophyll-a concentration (Chl-a) higher than 0.18 μg/L. The SST was the most important factor in the GAM analysis and the best fitting GAM model explained 67.9% of the variance. Understanding the biological characteristics and habitat status of S. oualaniensis in the SCS will benefit the management of this resource.

Despite the critical role of mitochondrial genomes (mitogenomes) in species identification and evolutionary studies in the genus Parupeneus, current resources are inadequate, given the species richness. Although previous studies have suggested a complex evolutionary history, the detailed mitogenomic variations and their implications remain largely unexplored. Therefore, we sequenced and assembled the mitogenomes of P. barberinoides, P. barberinus, P. biaculeatus, P. crassilabris, P. cyclostomus, P. heptacanthus, P. multifasciatus, and P. chrysopleuron, to enrich the molecular data and provide novel insights into the genetic diversity, evolutionary dynamics and phylogenetics of the family Mullidae. Our analysis revealed a novel gene rearrangement in P. chrysopleuron, Cytb-T-P-CR-Q-I-F-12S-V-16S-ND1-M-ND2, which differed from the conventional sequence of Cytb-T-P-CR-F-12S-V-16S-ND1-I-Q-M-ND2 observed in other species. In the novel rearrangement, four non-coding regions are inserted between ND1 and M, Q and I, I and ψM (tRNA-Met pseudogene), ψM and F. We assume that two tandem duplication/random loss events occur in the CR and IQM, making the entire sequence longer than that in other Parupeneus species. The phylogenetic results indicated that Mullidae formed a sister group relationship with the family Dactylopteridae, contradicting previous studies that identified a sister group relationship between Mullidae and Callionymoidei. The genera Parupeneus and Mullus formed a sister group, and discrepancies were found in the topological structure of the interspecies relationships within the genus Parupeneus compared with those reported by previous studies. Through combined phylogenetic and mitochondrial structural analysis, we found that phylogenetic topology is closely related to mitochondrial structural abnormalities. This study not only expands the mitogenomic dataset available for Mullidae but also underscores the importance of mitochondrial DNA studies in resolving taxonomic ambiguities and understanding the evolutionary history of marine fishes. Our study contributes to the ongoing research on marine fish taxonomy, mitogenomics, and evolutionary biology by providing new insights into the genetic diversity of marine ecosystems.

Hairtail (Scombriformes: Trichiuridae) have always ranked first in single-species production in Chinese marine fishery. However, due to the confusion of species identification, in official statistics, data on hairtail production and economic value are a combination of all the different species of Trichiuridae. In this study, based on sampling along China’s coastal areas, the composition and distribution of common hairtail species, as well as their age, growth, and trophic traits, are discussed. Six species of four genera and two subfamilies were identified, and largehead hairtail (Trichiurus japonicus) and Savalai hairtail (Lepturacanthus savala) were the most important populations that constituted catch production. The growth parameter b could be divided into two groups, with values in species mostly inhabiting northern parts of Chinese seas higher than those in southern parts. Most individuals were 1–2 years of age, suggesting species sexual precocity and individual miniaturization under multiple stresses. Species of Trichiuridae are at the top of the food web and play a bottom-up role in regulating the trophic dynamics of marine food webs. Largehead hairtail showed the highest stability and the greatest impact on the stability of the trophic structure. Despite temporary resource maintenance under fishery-induced evolution, the effective recovery and reasonable utilization of hairtail resources are still the main focuses of attention for Chinese marine fishery.

Fish early-stages constitute useful indicators of the states of marine ecosystems, as well as important fishery resources. Given the spectacular phenotypic changes during ontogeny, and the paucity of diagnostic morphological characters at the species level, the identification of fish early-stages is a challenging task. DNA barcoding, the use of the mitochondrial gene of the cytochrome c oxidase subunit I (COI) as an internal species tag, opened new perspectives for the identifications of both larval fish and fish eggs. However, the accuracy of the identifications assisted by DNA barcoding are dependent of the completeness of the DNA barcode reference libraries used to assigned unknown sequences to known species. Here, we built a DNA barcode reference library for 113 species of larval fish and 85 species of fish eggs involving the production of 741 newly generated DNA barcodes from South China Sea (63 localities). Together with 514 DNA barcodes mined from Genbank for 116 species from the South China Sea regions, a reference library including 1255 DNA barcodes for 308 species (248 locations) was assembled. The present study emphasizes the importance of integrating DNA barcoding to large scale inventories of early stages, as DNA-based species delimitation analyses delimited 305 molecular operational taxonomic units (MOTUs) and multiple cases of discordance with morphological identifications were detected. Cryptic diversity is detected with 14 species displaying two MOTUs and a total of 23 species were lumped into 11 MOTUs due to low interspecific divergence and/or mixed lineages.

The Beibu Gulf in China is situated in the tropics, in the western Pacific Ocean. It is an emblematic region combining proximity to a marine biodiversity hotspot and a major seafood hub. Intensification of marine fishing and ocean warming led to a drastic decline in fish populations in the Beibu Gulf during the last decades. This situation urges the development of molecular resources of the Beibu Gulf fish fauna in order to enable automated molecular identifications at the species level for next‐generation monitoring. With this objective, we present the results of a large‐scale campaign to DNA barcode fishes of the Beibu Gulf. We successfully generated 789 new DNA barcodes corresponding to 263 species which, together with 291 sequences mined from Genbank and BOLD, resulted in a reference library of 1080 sequences from 285 species. Based on the use of four DNA‐based species delimitation methods (BIN, ASAP, mPTP, mGMYC), a total of 285 Molecular Operational Taxonomical Units (MOTUs). A single case of cryptic diversity was detected in Scomberomorus guttatus and a single species pair was not captured by delimitation methods. Intraspecific K2P genetic distances averaged 0.36% among sequences within species, whereas K2P genetic distances among species within genera averaged 6.96%. The most speciose families in open water trawling differ from those at fish market, and discrepancies with historical data are discussed in the light of recently documented stock collapses.