Phylogeography and population structure of Lagocephalus spadiceus (Richardson, 1845) (Tetraodontiformes, Tetraodontidae) in the South China Sea.

The climate fluctuations during the Late Pleistocene significantly influenced the phylogeographic structure and historical dynamics of marine fishes in the marginal seas of the western Pacific Ocean. The puffer fish, Lagocephalus spadiceus, holds substantial nutritional and economic value in the South China Sea. To investigate the demographic history and population structure of the L. spadiceus, the mitochondrial DNA COI and Cyt b gene datasets from 300 individuals across eight populations in the South China Sea were sequenced. Our findings revealed high haplotype diversity (0.874 ± 0.013) and low nucleotide diversity (0.00075 ± 0.00058). The phylogenetic tree and haplotype networks revealed no significant genetic differentiation along the northern coast of South China Sea. Neutrality tests, mismatch distribution analyses, and Bayesian skyline plots suggested that L. spadiceus underwent population expansion during the Late Pleistocene. Both ocean currents and climate change significantly influenced the geographical distribution and genetic population structure of L. spadiceus.

The Sympatric Coexistence Mechanism: A Case Study of Two Penahia Species in the Beibu Gulf, South China Sea.

The study of trophic relationships among closely related species plays an important role in deepening our understanding of the resource utilization characteristics, differentiation patterns, and population dynamics of co-occurring species in the same habitat. This research uses two congeneric fish species, Pennahia pawak and Pennahia anea, as examples. Based on a stomach content analysis and a carbon-nitrogen stable isotope analysis, a comparative analysis of their feeding habits and trophic niches is conducted. Additionally, a spatial niche analysis is employed to explore the coexistence and competitive mechanisms between these two closely related fish species. The results show that specialized feeding habits mitigate intraspecific competition as the population densities increase. The carbon and nitrogen stable isotope analysis reveals variations in the feeding habits and trophic levels with body length, indicating adaptive shifts in prey selection. Despite similar food resources, niche differentiation arises due to differences in dominant prey, facilitating coexistence. Differences in spatial niche further contribute to niche separation and coexistence. In resource-limited environments, species such as Pennahia utilize trophic and spatial niche differentiation to collectively exploit resources and achieve coexistence, with implications for fishery management favoring Pennahia resource occupancy capabilities.

Dietary Shifts in the Adaptation to Changing Marine Resources: Insights from a Decadal Study on Greater Lizardfish (Saurida tumbil) in the Beibu Gulf, South China Sea.

Understanding dietary behavior during the individual development of marine predators and its temporal variations elucidates how species adapt to changes in marine resources. This is crucial for predicting marine predators' habitat selection and the natural population's responses to environmental changes. The authors conducted a comparative analysis of dietary shift strategies and trophic level variations in Greater lizardfish (Saurida tumbil) in the Beibu Gulf during two distinct periods (2010 and 2020) using stomach content and stable isotope analysis methods. Possible driving factors for these changes were also explored. Changes in the fishery community structure and the decline in the abundance of primary prey resources have led the S. tumbil population to diversify their prey species, utilize alternative resources, and expand their foraging space. However, the species' foraging strategy, characterized by chasing and preying on schooling and pelagic prey, promoted stability in their feeding behavior across spatial and temporal scales. The main prey items remained demersal and pelagic fish species, followed by cephalopods and crustaceans. Similar to other generalist fish species, ontogenetic dietary shifts (ODSs) indicated a partial transition towards larger prey items. However, the timing and magnitude of the ODSs varied between the two periods, reflecting life-history variations and adaptive adjustments to environmental changes. In comparison to 2010, the population's mean body length (BL) increased in 2020, and the proportion of the population feeding on pelagic-neritic prey significantly increased. However, the δ15N values were lower, indicating that the shift in the ecological niche of preferred prey from demersal to pelagic-neritic was the primary cause of the decrease in trophic levels. In the future, we will conduct further quantitative research integrating the spatiotemporal data of both predators and prey to clarify the relationships between marine predators' feeding behavior, trophic levels, and changes in prey community structure.

DNA barcoding the ichthyofauna of the Beibu Gulf: Implications for fisheries management in a seafood market hub.

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.

Levels and health risk assessment of potential toxic elements in three dominant fish species from the Beibu Gulf, South China Sea.

In this study, eight potential toxic elements (PTEs) and stable isotope ratios (δ13C and δ15N) were analyzed in three dominant fish species of the Beibu Gulf, namely Saurida tumbil, Pennahia macrocephalus and Upeneus sulphureus. The mean contents (mg/kg, dry weight) of As, Cd, Cr, Cu, Mn, Ni, Pb and Zn in the three species of fish were 10.94, 0.11, 0.55, 2.00, 5.80, 0.47, 0.39, 41.70, respectively. Cr, Mn and Pb showed potential biomagnification effects in fish bodies while Cu and Zn were biodiluted through the food chain. The results of the health risk assessment showed that the total hazard quotient (THQ) ranged from 0.11 to 0.32 and 1.34 to 1.70 and the total carcinogenic risk (TCR) ranged from 5.44 × 10-4 to 1.35 × 10-3 and 6.35 × 10-3 to 1.57 × 10-2 for adults and children, respectively. These results suggest that consumption of the three fish species by adults lead to carcinogenic health risks and consumption of the three fish species by children would result in significant adverse health effects.

Species Composition, Growth, and Trophic Traits of Hairtail (Trichiuridae), the Most Productive Fish in Chinese Marine Fishery.

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.

Genetic structure of the small yellow croaker (Larimichthys polyactis) across the Yellow Sea and the East China Sea by microsatellite DNA variation: implications for the division of management units.

The small yellow croaker, Larimichthys polyactis, is a commercial fish of the order Perciformes that mainly inhabit estuaries and coastal waters.In recent years, the resources and catch of L. polyactis have undergone huge fluctuations. To detect genetic variations caused by the fluctuation of resources, genetic diversity of L. polyactis in the coastal waters of China were analyzed in this study using microsatellite DNA marker. The results revealed high genetic diversity of this species. The STRUCTURE, DAPC and F ST results all indicated that there was no genetic structure consistent with the distribution pattern. Overall, our main findings are in agreement with previous studies, indicating that L. polyactis showed high genetic diversity and low genetic differentiation. Our results for high genetic connectivity among L. polyactis localities provide insights into the development of management strategies, that is, to manage this species as a single management unit.

Genetic pattern and demographic history of cutlassfish (Trichiurus nanhaiensis) in South China Sea by the influence of Pleistocene climatic oscillations.

Trichiurus nanhaiensis is one of the most important commercial fish species in the South China Sea. This study aimed to investigate the level of genetic variation and population genetic structure of T. nanhaiensis in the South China Sea for the first time, using 281 individuals collected from seven locations along the coast of mainland China, Taiwan, and Hainan Island. A high level of haplotype diversity and low nucleotide diversity were detected in the mitochondrial DNA cyt b gene and nuDNA RYR 3 gene. The overall expected heterozygosity (He = 0.693) among the seven populations ranged from 0.681 to 0.706 in microsatellite DNA data, which revealed high levels of genetic diversity. Significant genetic differentiation was found in Taidong populations in Taiwan, revealing the prevention of gene flow caused by the Kuroshio Current. Two major lineages based on the cyt b gene suggested that the Taiwan Strait acted as a geographic barrier for T. nanhaiensis during the glacier periods in the late Pleistocene. The Bayesian skyline plot also revealed that population demographic expansion of T. nanhaiensis was estimated to have occurred in 0.1 Mya. Our results indicated that all populations of T. nanhaiensis had experienced a recent genetic bottleneck following recent expansion based on ABC analysis.

Demographic history and population genetic structure of Anisakis pegreffii in the cutlassfish Trichiurus japonicus along the coast of mainland China and Taiwan.

Studying the genetic diversity of nematode parasite populations is crucial to gaining insight into parasite infection dynamics and informing parasite phylogeography. Anisakiasis is a zoonotic disease caused by the consumption of infectious third-stage larvae (L3) of Anisakis spp. carried by marine fish. In the present study, a total of 206 mitochondrial DNA sequences (cytochrome c oxidase 2, cox2) were used to study the genetic diversity, genetic structure, and historical demography of twelve A. pegreffii populations from Trichiurus japonicas along the coast of mainland China and Taiwan. Two distinct evolutionary lineages of A. pegreffii and no significant genealogical structures corresponding to sampling localities suggested that isolation in the marginal seas shaped their patterns of phylogeographic distribution along the coast of mainland China and Taiwan during glaciation with lower sea levels. Furthermore, pairwise FST values and AMOVA did not indicate any significant genetic differentiation among groups with no relation to the geographic area, which might be attributed to fewer barriers to gene flow as well as large population sizes. The results of the neutrality test, mismatch distribution, and Bayesian skyline plot analyses showed that entire population underwent population expansion during the late Pleistocene. Analysis of the demographic history revealed that A. pegreffii underwent historical lineage diversification and admixture due to secondary contact based on ABC analysis. The present research represents the first definitive population structure and demographic history across sampling locations of A. pegreffii along the coast of mainland China and Taiwan.

Characterization of the mitochondrial genome of parupeneus indicus (perciformes, mullidae).

Parupeneus indicus, a species in the family Mullidae, inhabits the coastal and inner lagoon reefs of the Indian and Pacific oceans. The mitochondrial genome of P. indicus is 16,566 base pairs in length and contains 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a D-loop control region. The overall base composition is 26.58% A, 24.83% T, 30.39% C, and 18.19% G, indicating an AT-rich profile (51.41%). Phylogenetic analysis based on the 13 PCGs revealed a close evolutionary relationship between P. indicus and P. barberinus. The data obtained in this study represent a valuable mitogenomic resource for population studies in the family Mullidae and will contribute to gaining a better understanding of the conservation genetics and environmental DNA of these fish.

Complete mitogenomes of four Trichiurus species: A taxonomic review of the T.lepturus species complex.

Four Trichiurus species, T.japonicus, T.lepturus, T.nanhaiensis, and T.brevis, from the coasts of the China Seas, have been identified and their entire mitochondrial genomes (mitogenomes) have been sequenced by next-generation sequencing technology. A comparative analysis of five mitogenomes was conducted, including the mitogenome of T.gangeticus. The mitogenomes contained 16.568-16.840 bp and encoded 36 typical mitochondrial genes (13 protein-coding, 2 ribosomal RNA-coding, and 21 transfer RNA-coding genes) and two typical noncoding control regions. Although tRNAPro is absent from Trichiurus mitogenomes, when compared with the 22 tRNAs reported in other vertebrates, the gene arrangements in the mitogenomes of the studied species are consistent with those in most teleost mitogenomes. The full-length sequences and protein-coding genes (PCGs) in the mitogenomes of the five species had obvious AT biases and negative GC skew values. Our study indicate that the specimens in the Indian Ocean are neither T.lepturus nor T.nanhaiensis but they are T.gangeticus; the Trichiurus species composition in the Indian Ocean is totally different from that in Pacific and Atlantic oceans; there are at least two Trichiurus species in Indian Ocean; and the worldwide systematics and diversity of the genus Trichiurus need to be reviewed.

Novel duplication remnant in the first complete mitogenome of Hemitriakis japanica and the unique phylogenetic position of family Triakidae.

In this study, we firstly determined the complete mitogenome of the Japanese topeshark (Hemitriakis japonica), which belong to the family Triakidae and was assessed as Endangered A2d on the IUCN Red List in 2021. The mitogenome is 17,301 bp long, has a high AT content (60.0%), and contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, a control region and specially a 594 bp-long non-coding region between Cytb gene and tRNA-Thr gene. The novel non-coding region share high sequence similarity with segments of the former and latter genes, so it was recognized as a duplication remnant. In addition, the Cytb gene and tRNA-Thr gene tandemly duplicated twice while accompanied by being deleted once at least. This is the first report of mitogenomic gene-arrangement in Triakidae. The phylogenetic trees were constructed using Bayesian inference (BI) and maximum likelihood (ML) methods based on the mitogenomic data of 51 shark species and two outgroups. In summary, basing on a novel type of gene rearrangements in houndshark mitogenome, the possibly rearranged process was analyzed and contributed further insight of shark mitogenomes evolution and phylogeny.

Changes in the trophic niche of Trichiurus japonicus in the Beibu Gulf in different periods.

We measured stable carbon and nitrogen isotopes and calculated trophic level and trophic niche of Trichiurus japonicus, with samples collected from the Beibu Gulf from 2008 to 2009 and 2018. The differences between two periods were compared and analyzed to explore the changes of its ecological adaptation. The results showed that value of δ13C varied substantially between the two periods. The narrowed range and the smaller mean value of δ13C in 2018 suggested that their food source changed from upper-middle to lower-middle waters. The values of δ15N were stable, and the range and mean values of trophic level (3.38-3.43) did not change significantly, which indicated a stable trophic level of T. japonicas in the past decade. The correlation between δ13C and preanal length was not significant, but a positive correlation between δ15N and preanal length. In terms of trophic niche, the indicators had decreased in different degrees in 2018 with 1.1%-32.1%. The value of total area and standard ellipse area decreased from 20.20 and 4.68 to 14.20 and 3.18, respectively, indicating that the niches of T. japonicas in the Beibu Gulf had varied obviously and that their ability to use resources and adapt to the environment had declined. It was speculated that in the past decade, the mean trophic level of T. japonicas in the Beibu Gulf had not changed significantly. Due to the change of food sources, however, the diversity of trophic sources had decreased, and the trophic niche had become smaller.

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Carbon and nitrogen stable isotope analysis was carried out on pelagic fishery organisms caught in light traps and falling nets in the central and western South China Sea in the spring of 2018. The stable isotope values of the sampled individuals were used to elucidate the isotopic variations for the pelagic fishery organisms, to classify species into trophic functional groups, and to compare the differences of trophic structure among the classified trophic functional groups. The results showed that among 23 fishery species the mean δ13C value of Coryphaena hippurus was the lowest (-17.58‰±0.21‰), and that of Grammistes sexlineatus was the highest (-19.86‰±0.33‰). The mean δ15N values ranged from 8.31‰ in Psenes cyanophrys to (12.46±0.74)‰ in Chirocentrus dorab. The continuous trophic spectrum indicated that the trophic level (TL) for the sampled pela-gic fishery organisms ranged from 3.01 to 4.23, of which 19 species (83% of the total) fell between TL 3.0 and 4.0. The 23 species of fishery organisms were classified into three trophic functional groups, i.e., plankton feeding functional group (PFFG), nekton feeding functional group (NFFG), and mixed feeding functional group (MFFG). The analysis of standard ellipse area (SEA) showed that the PFFG occupied the largest trophic niche width (SEA=1.56‰2), followed by the MFFG (SEA=0.99‰2) and NFFG (SEA=0.31‰2). The MFFG overlapped with PFFG and NFFG in the trophic niche, with a relative percentage of 17% and 26%, respectively. There was no overlap between PFFG and NFFG.

Characterization of the complete mitochondrial genome of Cynoglossus nanhaiensis (Pleuronectiformes: Cynoglossidae).

In this study, the complete mitochondrial genome of Cynoglossus nanhaiensis was determined. The total length of the mitochondrial genome is 17,130 bp, including 13 protein-coding genes, 22 tRNA genes, two rRNA genes, and two noncoding regions. The gene rearrangement of tRNAGln gene and control region (CR) were detected, forming a unique gene order of CR-Ile-Gln-Met. Maximum-likelihood and Bayesian inference method are used to perform the phylogenetic analysis, and the result reveals a close relationship between C. nanhaiensis and Cynoglossus itinus.

Characterization of the mitochondrial genome of Favonigobius reichei (Perciformes, Gobiidae).

Favonigobius reichei, belongs to the family Gobiidae, which is widely distributed in estuarine and marine waters of the coasts of the Indian and the western Pacific Oceans. The entire mitochondrial genome of F. reichei is 16,415 base pairs (bp) in length and contained 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, and 22 transfer RNA (tRNA) genes. The overall base composition is 27.71% A, 26.78% T, 28.02% C, and 17.49% G, showing AT-rich feature (54.49%). Phylogenetic analysis based on 13 PCGs shows the F. reichei has the closest evolutionary relationship with Myersina macrostoma. This work provides a valuable mitogenome resource for better understanding of the conservation genetics, environmental DNA, and population studies in the family Gobiidae.

Characterization of the complete mitochondrial genome of the coral reef fish, Hemigymnus melapterus (Pisces: Labridae) and its phylogenetic implications.

Hemigymnus melapterus belongs to the family Labridae, which inhabit in coastal and continental shelf waters. The entire mitochondrial genome of H. melapterus is 16,527 base pairs (bp) in length and contained 13 protein-coding genes, two rRNA genes, and 22 tRNA genes. The overall base composition is 27.56% A, 25.58% T, 30.02% C, and 16.85% G, showing AT-rich feature (53.14%). Phylogenetic analysis based on 13 protein-coding genes shows the H. melapterus has the closest evolutionary relationship with Stethojulis strigiventer. This work provides valuable genome variation information, which will be useful for phylogenetic analysis and population genetics research.

R language-based methods for revealing taxonomic and functional diversity and tracing process of fish fauna.

This paper presented the fish species richness at geographical unit of the Yangtze River. According to the fish taxonomic catalogs and biological traits, R language method was used to determine taxonomic diversity and functional diversity and the components of each unit. Regression analysis was used to test the varying tendency of taxonomic and functional diversity corresponding to the change of species richness. •Functional diversity is compared against taxonomic diversity in capturing the structure of dynamic ecosystem.•The ß-diversity indices of taxonomy and function were calculated and decomposed to evaluate the role of species turnover and nestedness in the formation process of fish spatial pattern.•An integrated diversity index, balancing α and ß diversity of species richness, taxonomic and functional diversity, is used to screen the prior conservation zone.

Dataset on the distribution location and biological traits of freshwater fishes in the Yangtze River Basin.

In this data article, we provide the scientific and theoretical data on fish taxonomy including class, order, family, and genus in the Yangtze River. The Yangtze basin is divided into 56 units, and their geological information including latitude, longitude, latitude, and channel length is recorded. Fish presence/absence data at the unit scale are reported. Biological traits including morphological, physiological, and ecological characters of each fish species are also described, numeralized, and reported. These data are the foundation of the analyses and results in the article "Continental-scale analysis of taxonomic and functional fish diversity in the Yangtze River" (Kang et al., 2018).

Influence of monsoonal winds on chlorophyll-α distribution in the Beibu Gulf.

The influence of seasonal, monsoonal winds on the temporal and spatial variability of chlorophyll-a (chl-a) in the Beibu Gulf is studied based on long-term satellite data of sea surface winds, chl-a concentration and sea surface temperature (SST) and in-situ observations for the years from 2002 to 2014. The analysis results indicated that under northeasterly monsoonal winds, chl-a concentrations were substantially elevated in most area of the Beibu Gulf, with a high chl-a concentration (>2 mg m-3) patch extending southwestward from the coastal water of the northeastern Gulf, consistent with the winter wind pattern. Meanwhile, the spatial distribution of high chl-a concentration is correlated with low SST in the northeastern Gulf. In the southern Gulf, there was generally low chl-a, except in the coastal waters southwest of Hainan Island. Here, the upwelling cold water prevails outside the mouth of the Beibu Gulf, driven by the southwesterly monsoonal winds and the runoff from the Changhua River, as implied by low observed SST. Correlation analysis indicated the chl-a concentration was strongly modulated by wind speed (r = 0.63, p<0.001), particularly in the middle of the northern Gulf and southern Hainan Island (r>0.7, p<0.001). Integrated analysis also showed that stratification is weak and mixing is strong in winter as affected by the high wind speed, which suggests that the wind-induced mixing is a dominant mechanism for entrainment of nutrients and the spatial distribution of chl-a in winter.