Stock Assessment of the Commercial Small Pelagic Fishes in the Beibu Gulf, the South China Sea, 2006-2020.

Long-term variations in population structure, growth, mortality, exploitation rate, and recruitment pattern of two major commercial small pelagic fishes (CSPFs) (Decapterus maruadsi and Trachurus japonicus) are reported based on bottom trawl survey data collected during 2006-2020 in the Beibu Gulf, South China Sea. All individuals collected during each sampling quarter over a period of 15 years were subjected to laboratory-based analysis. In this study, the stock of D. maruadsi and T. japonicus inhabiting the Beibu Gulf was assessed using length-based methods (bootstrapped electronic length frequency analysis (ELEFAN)) to complete stock assessment in different fishery management periods (the division of fisheries management periods was based on China's input and output in the South China Sea offshore fisheries over 15 years, specifically divided into period I (2006-2010), period II (2011-2015), and period III (2016-2020)). The results showed that the mean body length, dominant body size, and estimated asymptotic length of two CSPFs decreased, whereas their growth coefficient decreased, indicating miniaturization and slower growth, respectively. Estimated exploitation rates and catching body length for two CSPFs indicated that both stocks in the Beibu Gulf were overexploited in period I and moderately exploited after 2011. These stocks were taking a good turn in status in period III, with the exploitation rate much lower than the initial period and reversing the downward trend in catching body length. Furthermore, the variations in the spawning season of the two CSPF stocks and their barely satisfactory expected yield indicated the complexity of the current fishery management in the Beibu Gulf. These results suggest that management measures to reduce fishing pressure may have a positive influence on the biological characteristics of those CSPFs in the Beibu Gulf; however, the stock structure already affected by overfishing will be a huge challenge for the conservation and restoration of fisheries resources in the future. Given that the current stocks of D. maruadsi and T. japonicus in the Beibu Gulf still have low first-capture body length (Lc) and high fishing mortality (F) (compared to F0.1), we identify a need to refine population structure by controlling fishing efforts and increasing catchable size, and more consideration should be given to the local fishery resource status in fisheries management.

Feeding ecology of the short-headed lanternfish Diaphus brachycephalus and Warming's lanternfish Ceratoscopelus warmingii (Myctophidae) in the South China Sea.

We report on the feeding ecology of two species, the short-headed lanternfish Diaphus brachycephalus and Warming's lanternfish Ceratoscopelus warmingii, using data collected over five surveys from 2015 to 2017 in the open South China Sea. D. brachycephalus feed mainly on copepods, with few differences in food composition between different-sized individuals; the diet of C. warmingii is more diverse, including crustacean zooplankton, gelatinous animals, and Mollusca, and differs significantly between fishes >55 mm in body length and smaller fishes. Interspecific competition for food between these two species is not strong, while intraspecific competition may be more intense in D. brachycephalus than in C. warmingii. Trophic levels of D. brachycephalus (3.46) and C. warmingii (3.38) identify both species as third-trophic-level lower carnivores. The diel feeding patterns of D. brachycephalus and C. warmingii differ: the former feeds actively both day and night when food is plentiful, and feeds primarily in the upper layer at night and in the mesopelagic layer during the daytime, and the latter ascends into the upper 100 m at night to feed, but stomach fullness is lower than D. brachycephalus. Dry-body-weight daily ration estimates for D. brachycephalus range from 5.19% to 16.46%, and those for C. warmingii range from 1.38% to 4.39%.

Migration Route of Sthenoteuthis oualaniensis in the South China Sea Based on Statolith Trace Element Information.

Sthenoteuthis oualaniensis (Lesson, 1830) is a pelagic species with a complex population structure and wide migration range. The trace elements in statoliths are effective indicators for reconstructing the life history of an individual. In this study, the trace elements in statoliths were determined via laser ablation inductively coupled plasma mass spectrometry, and a multiple regression tree (MRT) model was used to trace the migration of S. oualaniensis and identify its potential habitats in the South China Sea. Na, Mg, Fe, Sr, and Ba were the effective trace elements, with significant differences found among stocks (p < 0.05). The MRT was divided into five clusters representing five life history stages. The Mg:Ca and Sr:Ca ratios decreased initially and increased thereafter, and the Mg:Ca, Sr:Ca, and Ba:Ca ratios differed significantly among the stages of the life history in each stock (p < 0.05). The hatching water temperatures for the winter and summer-autumn spawning populations were 28.05-28.88 °C (temperature at 25 m) and 27.15-27.92 °C (temperature at 25 m). The winter stock hatched in the southern South China Sea, and the larvae then migrated northwest during the summer monsoon. The summer-autumn stocks hatched in the northern South China Sea, and the larvae migrated southward under the mesoscale closed anticyclonic circulation in the northern South China Sea. These results provide insight into the migration of S. oualaniensis in the South China Sea.

Stable isotopic and stomach content analyses reveal changes in the trophic level and feeding habit of large-head hairtail (Trichiurus lepturus) in the northern South China Sea.

The feeding habit of large-head hairtail (Trichiurus lepturus) in the northern South China Sea was investigated through isotopic and stomach content analyses. The isotopic features of the hairtail at the same body size differed among regions, with the fish in coastal waters presenting higher δ15N and δ13C values compared to those in the open sea, indicating different trophic levels (TL), food habits, and isotopic baselines. According to the partial correlation of water depth with δ15N values, the sampling stations were divided into three regions based on the depth of water: coastal (20-40 m), near coastal (60-80 m), and open sea (100-200 m) regions. In the coastal region, the hairtail from stations affected by the Pearl River plume exhibited lower δ15N and δ13C values. The stomach content analysis indicated different feeding habits of the hairtail from different regions. The hairtail in the coastal and near coastal waters fed more on fish and less on crustaceans compared to the hairtail in the open sea. The relationship between δ15N and fish size exhibited two contrary patterns. First, the δ15N values increased with increasing preanal length in the hairtail sampled from the water depth of 30-40 m in section F (in fish with preanal length < 200 mm) and those samples from the water depth of 100-200 m. This finding reflected an ontogenetic shift in diet and TL. However, the δ15N values tended to decrease with the increasing preanal length of the hairtail samples collected from the water depth of 30-40 m in section F (fish with a preanal length of ~200-300 mm). These findings suggested that under the conditions of insufficient availability of high-quality prey, the larger hairtail fed more on low-TL prey to compensate for the increase energy demand, arising due to growth, which led to the observed decrease in δ15N values.

Impacts of Strong ENSO Events on Fish Communities in an Overexploited Ecosystem in the South China Sea.

To better understand how fish communities respond to environmental changes under extreme climate events, we examine changes in fish communities in Beibu Gulf during strong El Niño and La Niña events. Strong La Niña and El Niño events affect the composition, abundance, and distribution of fish communities in Beibu Gulf. Fish community distribution and composition change before and after La Niña and El Niño events, and dominant species within them change with stable fishing intensity. The abundance and distribution of small pelagic fish such as Japanese jack mackerel (Trachurus japonicus) and Japanese scad (Decapterus maruadsi) are the most affected. Using a generalized additive model (GAM), we explore relationships between the abundance of T. japonicus and D. maruadsi and a suite of environmental variables. The GAM results revealed that sea surface salinity and sea surface temperature best explain changes in catch per unit effort of these two species during a La Niña event; depth, sea surface temperature, and mixed layer depth during an El Niño event. The results obtained in this study will offer support for implementing more-accurate, scientific fisheries management measures.

Genomes of Two Flying Squid Species Provide Novel Insights into Adaptations of Cephalopods to Pelagic Life.

Pelagic cephalopods have evolved a series of fascinating traits, such as excellent visual acuity, high-speed agility, and photophores for adaptation to open pelagic oceans. However, the genetic mechanisms underpinning these traits are not well understood. Thus, in this study, we obtained high-quality genomes of two purpleback flying squid species (Sthenoteuthis oualaniensis and Sthenoteuthis sp.), with sizes of 5450 Mb and 5651 Mb, respectively. Comparative genomic analyses revealed that the S-crystallin subfamily SL20-1 associated with visual acuity in the purpleback flying squid lineage was significantly expanded, and the evolution of high-speed agility for the species was accompanied by significant positive selection pressure on genes related to energy metabolism. These molecular signals might have contributed to the evolution of their adaptative predatory and anti-predatory traits. In addition, the transcriptomic analysis provided clear indications of the evolution of the photophores of purpleback flying squids, especially the recruitment of new genes and energy metabolism-related genes which may have played key functional roles in the process.

A method to analyze the sensitivity ranking of various abiotic factors to acoustic densities of fishery resources in the surface mixed layer and bottom cold water layer of the coastal area of low latitude: a case study in the northern South China Sea.

This is an exploratory analysis combining artificial intelligence algorithms, fishery acoustics technology, and a variety of abiotic factors in low-latitude coastal waters. This approach can be used to analyze the sensitivity level between the acoustic density of fishery resources and various abiotic factors in the surface mixed layer (the water layer above the constant thermocline) and the bottom cold water layer (the water layer below the constant thermocline). The fishery acoustic technology is used to obtain the acoustic density of fishery resources in each water layer, which is characterized by Nautical Area Scattering Coefficient values (NASC), and the artificial intelligence algorithm is used to rank the sensitivity of various abiotic factors and NASC values of two water layers, and the grades are classified according to the cumulative contribution percentage. We found that stratified or multidimensional analysis of the sensitivity of abiotic factors is necessary. One factor could have different levels of sensitivity in different water layers, such as temperature, nitrite, water depth, and salinity. Besides, eXtreme Gradient Boosting and random forests models performed better than the linear regression model, with 0.2 to 0.4 greater R2 value. The performance of the models had smaller fluctuations with a larger sample size.

Complete Mitogenomes of Three Carangidae (Perciformes) Fishes: Genome Description and Phylogenetic Considerations.

Carangidae are ecologically and economically important marine fish. The complete mitogenomes of three Carangidae species (Alectis indicus, Decapterus tabl, and Alepes djedaba) were sequenced, characterized, and compared with 29 other species of the family Carangidae in this study. The length of the three mitogenomes ranged from 16,530 to 16,610 bp, and the structures included 2 rRNA genes (12S rRNA and 16S rRNA), 1 control region (a non-coding region), 13 protein-coding genes, and 22 tRNA genes. Among the 22 tRNA genes, only tRNA-Ser (GCT) was not folded into a typical cloverleaf secondary structure and had no recognizable DHU stem. The full-length sequences and protein-coding genes (PCGs) of the mitogenomes of the three species all had obvious AT biases. The majority of the AT-skew and GC-skew values of the PCGs among the three species were negative, demonstrating bases T and C were more plentiful than A and G. Analyses of Ka/Ks and overall p-genetic distance demonstrated that ATP8 showed the highest evolutionary rate and COXI/COXII were the most conserved genes in the three species. The phylogenetic tree based on PCGs sequences of mitogenomes using maximum likelihood and Bayesian inference analyses showed that three clades were divided corresponding to the subfamilies Caranginae, Naucratinae, and Trachinotinae. The monophyly of each superfamily was generally well supported. The divergence time analyses showed that Carangidae evolved during three geological periods, the Cretaceous, Paleogene, and Neogene. A. indicus began to differentiate from other species about 27.20 million years ago (Mya) in the early Miocene, while D. tabl (21.25 Mya) and A. djedaba (14.67 Mya) differentiated in the middle Oligocene.

Long-term variations in fish community structure under multiple stressors in a semi-closed marine ecosystem in the South China Sea.

Daya Bay is an ecologically and economically crucial semi-closed bay along the southern coast of China. It is proven to be a stressed ecosystem and therefore obviously vulnerable to further extrinsic disturbance. This study used fish data from bottom-trawl surveys, conducted from 1985 to 2018, to analyze variations in the fish community structure over the past 30 years. The results showed that warm-water fish species were overwhelmingly dominant during all years, suggesting the bay's tropical to subtropical characteristic. By 2015, the number of fish species had decreased by 29.44% of that caught in 1987, moreover, values of the Shannon-Wiener diversity index and the Margalef richness index were lower in 2015 compared to 2004. There were evident shifts in the fish community composition from pelagic to demersal species, as suggested by the dominant species found in springtime, the dominant families, and percentages denoting the numbers of species in the main orders. Average fish body weight in landings declined from 13.4 g to 7.58 g, the body sizes of four typical commercial fish species decreased by varying degrees over the last 30 years. Abundance-biomass comparison curves suggested that the Daya Bay fish community was more stressed in 2015 than in 2004 during all seasons, except winter. In general, the fish community structure in Daya Bay is consequently in an unsteady state. Multiple anthropogenic disturbances, such as fishing (including overfishing and changes in the main fishing gears), the destruction of natural habitats, pollutants, and anthropogenically induced temperature changes, are likely to have caused obvious shifts in the bay's fish community structure. Therefore, we emphasize the need for integrating management of multiple anthropogenic stressors to achieve ecosystem-based management.

Population dynamics of threadfin porgy Evynnis cardinalis, an endangered species on the IUCN red list in the Beibu Gulf, South China Sea.

Threadfin porgy Evynnis cardinalis is both a dominant fish species and an important fishing target in bottom trawl fisheries in the Beibu Gulf, South China Sea. It was listed as endangered (EN) in a recent International Union for Conservation of Nature (IUCN) red list. Despite its economic importance and endangered status, limited research on its biological characteristics and spatial-temporal distribution has been undertaken this last decade, creating uncertainty in current conservation and management. We analyse this species' spatial distribution characteristics using data from four seasonal bottom trawl surveys in 2014-2015, and report average catch per unit effort to vary seasonally, from 49.1 to 594.5 ind h-1 . Growth, mortality and sexual maturity are reported for four time periods based on data from bottom trawl fishery surveys over 1961-1962, 1998-1999, 2006, and 2014-2015. Length frequency distributions changed from bimodal to unimodal, and the female-to-male ratio increased. Mean body length and length at first maturity decreased, whereas the growth coefficient increased, indicating miniaturization, early sexual maturity and accelerated growth, respectively. We report sparid catch to have first exceeded maximum sustainable yield in 2001, and to have remained overfished from 2010 to 2015. Since the 1980s, low-trophic-level fishes such as E. cardinalis have replaced high-trophic-level fishes such as Crimson snapper Lutjanus erythropterus to become dominant species. As catches have increased substantially, these species have been faced with overfishing, driving the ecosystem into an unstable state.

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To understand the relationships among dominant species of cephalopods in offshore nor-thern South China Sea, we examined the niche characteristics of these dominant species from both spatial and temporal dimensions using the index of relative importance (IRI), the niche breadth and overlap indices based on fishery resources data from the bottom-trawl survey for four seasons during 2014-2015. The results showed that five dominant species of cephalopods were recorded for four seasons, including Loligo edulis, L. chinensis, L. beka, Sepia esculenta, and L. duvaucelii. The first two species were shared by all seasons. Compared with historical data, the composition of dominant cephalopods species had changed. The cephalopods resource exhibited obvious temporal and spatial variations. Stock density was higher in the sea area extending from the southern Hainan Island to eastern Guangdong Province than that in Beibu Gulf. The seasonal variation was characte-rized by the largest in summer but the smallest in winter. The temporal and spatial niche analysis showed that there was inconsistent in the order between temporal and spatial niche breadths for domi-nant species. L. edulis (1.32) and L. chinensis (3.90) occupied the largest temporal and spatial niche breadths, respectively. The smallest of temporal and spatial niche breadths were shown for S. esculenta (0.98) and L. duvaucelii (2.04), respectively. Though the temporal niche overlap was numerically larger than the spatial niche overlap, both of them had higher values in interspecies among L. edulis, L. chinensis, L. beka, and the lower overlap for the species pairs between L. duvaucelii and other species. The result of correlation analysis suggested that niche breadth exhibited a significant negative correlation with variation in abundance on both temporal and spatial scales. The ecological niche could reflect the tempo-spatial changes of species resource, which enriched the traditional methods of fishery communities.

Synechococcus bloom in the Pearl River Estuary and adjacent coastal area-With special focus on flooding during wet seasons.

Based on the field surveys aimed at understanding the variations of Synechococcus (Syn) abundance in the Pearl River Estuary during different seasons. We found that heavy terrestrial precipitation result in significant riverine runoffs and promote Syn growth, extension and blooms during warm and wet seasons. To understand the ecological role of Syn play in this estuary during wet seasons, we combined flow cytometry and high throughput sequencing (HTS) of 16S rDNA to investigate the phytoplankton distribution patterns and the potential shaping mechanisms during a typical wet season. During the cruise, picophytoplankton, especially Syn, and Nano-eukaryotes contributed importantly to the total phytoplankton biomass of the estuary. Syn can be further divided into phycoerythrin (PE)-rich Syn and phycocyanin (PC)-rich Syn, with PC-rich Syn about 1.5 times higher than PE-rich Syn in abundance. Both PE-rich Syn (60.75 × 103 cells ml-1) and PC-rich Syn (604.05 × 103 cells ml-1) reach the highest abundance at the lower part of the estuary. Moreover, PE-rich Syn can be divided into two subgroups which showed different salinity preference, with PE1 distributed in the high salinity area (with salinity >25) while PE2 in the middle salinity area (with salinity 7-20). Our results from the 16S rDNA sequencing also indicated abundant diversity and different niche adaptation of Syn with the operational taxonomic units (OTUs) along the estuary. Besides, analysis also indicated a tight correlation between estuarine Syn and active heterotrophic bacteria, especially groups of Rhodobacteria and Actionobacteria.

Transcriptomic analyses of gastrointestinal function in the "dwarf" and "medium" forms of Sthenoteuthis oualaniensis during sexual maturation.

Sthenoteuthis oualaniensis (SA) is an important squid species in the South China Sea. Based on SA samples collected in 2016, SA was divided into the "dwarf" form (DF) and "medium" form (MF). To understand the changes in gastrointestinal function in SA during sexual maturation, we undertook transcriptomic analyses of the stomach and intestine tissues of the mature and immature DF and MF of SA using the deep-sequencing platform Illumina HiSeq™. We exploited a high-throughput method to delineate differentially expressed genes (DEGs) in the DF and MF of SA. A total of 135464 unigenes (68627 unigenes of the DG and 66837 unigenes of the MF) were generated. We identified 7965 and 4051 relative DEGs in the intestine and stomach tissues of the mature DF of SA compared with those of the immature DF of SA; and 22138 and 18460 DEGs in the intestine and stomach of the mature MF of SA compared with those of the immature MF of SA. Gastrointestinal function related to the metabolism of lipids, amino acids, glucose, and energy were changed in SA during sexual maturation. This work is the first to identify a set of genes associated with gastrointestinal function during sexual maturation in SA.

Spatial and seasonal distributions of bacterioplankton in the Pearl River Estuary: The combined effects of riverine inputs, temperature, and phytoplankton.

In this study, we used flow cytometry and 16S rRNA gene pyrosequencing to investigate bacterioplankton (heterotrophic bacteria and picocyanobacteria) abundance and community structure in surface waters along the Pearl River Estuary. The results showed significant differences in bacterioplankton dynamics between fresh- and saltwater sites and between wet and dry season. Synechococcus constituted the majority of picocyanobacteria in both seasons. During the wet season, Synechococcus reached extremely high abundance at the mouth of the estuary, and heterotrophic bacteria were highly abundant (>106cellsml-1) throughout the studied region. At the same time, bacterioplankton decreased dramatically during the dry season. Pyrosequencing data indicated that salinity was a key parameter in shaping microbial community structure during both seasons. Phytoplankton was also an important factor; the proportion of Synechococcus and Rhodobacteriales was elevated at the frontal zone with higher chlorophyll a during the wet season, whereas Synechococcus were markedly reduced during the dry season.

Complete mitochondrial genome of the African pompano Alectis ciliaris (Perciformes: Carangidae).

The African pompano Alectis ciliaris (Perciformes: Carangidae) is an economic fish species distributed throughout the tropical oceans and seas of the world. In this study, we assembled the complete mitochondrial genome of A. ciliaris from contiguous, overlapping segments amplified by polymerase chain reactions. The complete mitogenome sequence was 16,570 bp in length, consisting of 37 typical animal mitochondrial genes and 1 control region, same with the typical vertebrate mitochondrial gene arrangement. There were 10 regions of gene overlaps totaling 30 bp and 12 intergenic spacer regions totaling 67 bp. The overall base composition of the heavy strand was 28.32% for A, 26.77% for T, 16.16% for G, 28.75% for C with a slight AT bias of 55.09%.

Mitochondrial genome of the Torpedo scad Megalaspis cordyla (Perciformes: Carangidae): genome characterization and phylogenetic consideration.

This study presented the complete mitochondrial genome of the Torpedo scad Megalaspis cordyla, the only member of its genus, as well as its phylogenetic position in Carangidae. The genome is 16,566 bp containing the usual 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, and 1 control region. Gene organization is similar to that observed in most other vertebrates. Gene overlapping and separating were also observed in M. cordyla mitogenome. The overall base compositions of mitogenome was 28.83% A, 25.81% T, 15.93% G, and 29.43% C. Phylogenetic analyses using the concatenated sequence of the protein-coding genes of the reported Carangidae mitogenome showed similar results in the neighbour-joining and Bayesian inference trees. Three clades were formed as Subfamilies Caranginae, Seriolinae and Trachinotinae in Carangidae. M. cordyla was most closely related to the species in genus Caranx.

Description of the mitochondrial genome of yellowtail scad Atule mate (Perciformes: Carangidae).

The yellowtail scad Atule mate is an economic fish species distributed throughout the tropical and subtropical oceans of the Indo-Pacific region. In the present study, we assembled the complete mitochondrial genome of A. mate from contiguous, overlapping segments amplified by PCR. The mitogenome sequence was 16,565 bp in length, consisting of 37 typical animal mitochondrial genes and 1 control region, same with the typical vertebrate mitochondrial gene arrangement. The overall base composition of the heavy strand was 28.4% for A, 27.6% for T, 16.3% for G, and 27.7% for C. Phylogenetic analyses using the protein-coding gene sequences reveal that genus Atule was most closely related to Alepes.

Mitochondrial genome of the Mackerel scad Decapterus macarellus (Perciformes: Carangidae).

The complete mitochondrial genome sequence was determined for the Mackerel scad Decapterus macarellus, one species of the economically important fish in Carangidae. The entire sequence of the genome was 16,544 bp in length, including the typical structure of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 non-coding control region. Overall base compositions of the sequence were 27.3% of A, 30.4% of C, 25.3% of T and 17.0% of G, showing an obvious anti-G bias commonly observed in teleosts. The mitogenome of Decapterus macarellus had a quite high-sequence similarity (92.5%) with D. macrosoma, which was morphologically close to D. macarellus. The complete mitogenome sequence data of D. macarellus could provide useful information for taxonomic and phylogenetics studies.

The complete mitochondrial genome of longfin yellowtail S. rivoliana (Perciformes: Carangidae).

The complete mitochondrial genome of the longfin yellowtail Seriola rivoliana (Perciformes: Carangidae) was obtained in this study. The entire genome was sequenced via primer walking after long PCRs. The size of the genome was 16,530 bp in length, containing the usual 2 rRNA genes, 13 protein-coding genes, 22 tRNA genes, and one non-coding control region. The genome composition and gene order were similar to most vertebrates. Most mitochondrial genes (excepted for ND6 and eight tRNA genes) were encoded on the heavy strand. The complete mitogenome of S. rivoliana could provide a basic data for studies on species identification, molecular systematics and conservation genetics.

Characterization of the mitochondrial genome of the Shortfin scad Decapterus macrosoma (Perciformes: Carangidae).

The complete mitochondrial genome sequence of Decapterus macrosoma has been obtained with overlapped polymerase chain reaction. The genome was 16,545 bp in length which contained 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 2 non-coding regions (the control region and the light strand replication origin). Gene organization was similar to that observed in most other vertebrates. With the exception of the ND6 and eight tRNA genes, all other genes were encoded on the heavy strand. The genome was composed of 27.0% A, 30.4% C, 25.4% T and 17.2% G, showing an obvious anti-G bias commonly observed in teleosts. Two termination-associated sequence regions (TAS-1 and TAS-2), three central conserved sequence blocks (CSB-F, CSB-E and CSB-D), and three conserved sequence blocks (CSB-1, CSB-2 and CSB-3) were identified within the control region. The sequence data of D. macrosoma could provide useful information for the studies on molecular systematics and population genetics.