First pelagic fish biodiversity assessment of Cosmonaut Sea based on environmental DNA.

The Cosmonaut Sea is a typical marginal sea in East Antarctica that has not yet been greatly impacted by climate change. As one of the least explored areas in the Southern Ocean, our knowledge regarding its fish taxonomy and diversity has been sparse. eDNA metabarcoding, as an emerging and promising tool for marine biodiversity research and monitoring, has been widely used across taxa and habitats. During the 38th Chinese Antarctic Research Expedition (CHINARE-38), we collected seawater and surface sediment samples from 38 stations in the Cosmonaut Sea and performed the first, to our knowledge, eDNA analysis of fish biodiversity in the Southern Ocean based on the molecular markers of 12S rRNA and 16S rRNA. There were 48 fish species detected by the two markers in total, with 30 and 34 species detected by the 12S rRNA and 16S rRNA marker, respectively. This was more than the trawling results (19 species) and historical survey records (16 species, "BROKE-West" cruise). With some nonsignificant differences between the Gunnerus Ridge and the Oceanic Area of Enderby Land, the Cosmonaut Sea had a richer fish biodiversity in this research compared with previous studies, and its overall composition and distribution patterns were consistent with what we know in East Antarctica. We also found that the eDNA composition of fish in the Cosmonaut Sea might be related to some environmental factors. Our study demonstrated that the use of the eDNA technique for Antarctic fish biodiversity research is likely to yield more information with less sampling effort than traditional methods. In the context of climate change, the eDNA approach will provide a novel and powerful tool that is complementary to traditional methods for polar ecology research.

Comparative transcriptome sequencing analysis of female and male Decapterus macrosoma.

Sexual growth dimorphism is a common phenomenon in teleost fish and has led to many reproductive strategies. Growth- and sex-related gene research in teleost fish would broaden our understanding of the process. In this study, transcriptome sequencing of shortfin scad Decapterus macrosoma was performed for the first time, and a high-quality reference transcriptome was constructed. After identification and assembly, a total of 58,475 nonredundant unigenes were obtained with an N50 length of 2,266 bp, and 28,174 unigenes were successfully annotated with multiple public databases. BUSCO analysis determined a level of 92.9% completeness for the assembled transcriptome. Gene expression analysis revealed 2,345 differentially expressed genes (DEGs) in the female and male D. macrosoma, 1,150 of which were female-biased DEGs, and 1,195 unigenes were male-biased DEGs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the DEGs were mainly involved in biological processes including protein synthesis, growth, rhythmic processes, immune defense, and vitellogenesis. Then, we identified many growth- and sex-related genes, including Igf, Fabps, EF-hand family genes, Zp3, Zp4 and Vg. In addition, a total of 19,573 simple sequence repeats (SSRs) were screened and identified from the transcriptome sequences. The results of this study can provide valuable information on growth- and sex-related genes and facilitate further exploration of the molecular mechanism of sexual growth dimorphism.

Effects of oceanographic environment on the distribution and migration of Pacific saury (Cololabis saira) during main fishing season.

The Pacific saury (Cololabis saira) is one of the most commercially important pelagic fishes in Asia-Pacific countries. The oceanographic environment, especially the Oyashio Current, significantly affects the distribution of Pacific saury, and may lead to variations in their migration route and the formation of fishing grounds in Japanese coastal region and the high seas. In this study, six oceanographic factors, sea surface temperature (SST), sea surface chlorophyll-a concentration (SSC), sea surface salinity (SSS), sea surface height (SSH), mixed layer depth (MLD), and eddy kinetic energy (EKE), were associated with the monthly catch per unit effort 1 (monthly CPUE1, ton/vessel) and the monthly CPUE2 (ton/day) of Pacific saury from Chinese fishing vessels during the optimal fishing periods (September-November) in 2014-2017. The gradient forest analysis showed that the performance of monthly CPUE1 was higher than monthly CPUE2 and SST was the most important oceanographic factor influencing monthly CPUE1, followed by EKE. The generalized additive model indicated that SST, SSH, and EKE negatively affected monthly CPUE1, whereas SSC, SSS, and MLD induced dome-shaped increases in monthly CPUE1. The distributions of fishing locations are likely to form along Offshore Oyashio current and meanders, especially in October and November. Synchronous trends in the relationship between the intrusion area of the Oyashio and relative abundance variation index suggest that an increase in the intrusion area of the Oyashio causes more Pacific saury to migrate to the Japanese coastal region, and vice versa. These findings extend our understanding of the effects of the oceanographic environment on Pacific saury.

Spatio-temporal variation of microplastic pollution in the sediment from the Chukchi Sea over five years.

Sediment has been considered as an important sink for microplastics (MPs), but there are limited reports about the spatial and temporal variability of MPs in sediment from the Arctic Ocean. Furthermore, understanding is lacking on the correlation between Arctic sea ice variation and MP abundance in sediment. This study aimed to assess the MP contamination in the sediment from the Chukchi Sea over five years through three voyages (in 2016, 2018, and 2020). The MP abundances in the sediments from the Chukchi Plateau and Chukchi Shelf over five years ranged from 33.66 ± 15.08 to 104.54 ± 28.07 items kg-1 dry weight (DW) and 20.63 ± 6.71 to 55.64 ± 22.61 items kg-1 DW, respectively. The MP levels from the Chukchi Sea were lower than those from the Eastern Arctic Ocean. Our findings suggest that the Chukchi Plateau is an accumulation zone for fibers related to fishing gear and textiles under the dual influence of the Pacific and Atlantic Ocean currents. However, the reduction of these fibers in the sediment from the Chukchi Shelf might be related to bottom currents, sediment resuspension, and biomass. Moreover, the MP abundance in the sediment from the Chukchi Sea was positively correlated with the reduction of Arctic sea ice, suggesting that the melting sea ice contributes to the increase in MP levels in the sediment. The increase in blue MPs from the Chukchi Plateau over time might be attributed to melting sea ice or intense fishing activity, whereas the increase of the smallest MPs in this region could be owing to the breakdown of larger plastics during long-distance transport or the easier settlement of smaller MPs. Further time-series investigations are urgently required to improve the understanding of the environmental fate and transport of MPs among the different Arctic environmental compartments.

New perspective on the genetic structure and habitat adaptation of Pampus minor off the coast of China based on RAD-seq.

Understanding the genetic diversity and habitat adaptation patterns of different geographic populations of marine organisms is essential for the rational maintenance, development, and utilization of their resources. Pampus minor Liu and Li 1998 is an economically valuable marine fish species. To determine the population genetic structure and elucidate the genetic mechanism underlying the habitat adaptation of this species, restriction site-associated DNA sequencing (RAD-seq) was used to scan the whole genomes of three P. minor putative populations along the coast of China for single-nucleotide polymorphism (SNPs) and outlier SNPs. Our population genetic structure analysis based on 2388 SNPs and 731 outlier SNPs throughout the genome revealed no significant genetic differentiation among the three populations. Results suggested that the life-cycle characteristics of P. minor, its relatively large population sizes, and ocean current transport might have shaped its current genetic pattern. The annotation information of both assembled sequences (which included outlier SNPs) and candidate loci associated with adaptations indicated that genes involved in many processes, including ion exchange, osmotic pressure regulation, metabolism, and the immune response, have been very important in the adaptations of P. minor to its heterogeneous habitats. Against the background of increased human activities, increased fishing intensity, and destruction of marine habitats, the results of this study provide basic genetic information for the accurate division of protection units of P. minor.

Microplastic pollution in wild commercial nekton from the South China Sea and Indian Ocean, and its implication to human health.

Marine biota, especially commercially important species, serves as a basis for human nutrition. However, millions of tons of plastic litter are produced and enter the marine environment every year, with potential adverse impacts on marine organisms. In the present study, we investigated the occurrence and characteristics of microplastic (MP) pollution in the digestive tracts of 13 species of wild nektons from 20 stations sampled in the South China Sea (SCS) and the Indian Ocean (IO), and assessed the human health risks of MPs. The detection rate of MPs ranged from 0.00% to 50.00% from the SCS, which was dramatically lower than that from the IO (10.00-80.00%). The average abundance of MP was 0.18 ± 0.06 items g wet weight-1 (ww-1) in the SCS, which was significantly lower than that in the IO with a concentration of 0.70 ± 0.16 items g ww-1. Most MPs were fibers in type, black in color, and polyester (PES) in polymer composition in both the SCS and IO. Interestingly, distinct profiles of MP pollution were found between the benthic and pelagic nektons: 1) The predominant MP composition was PES in the benthic nektons, whereas polyamide (PA) accounted for a larger part of the total MP count in the pelagic nektons within the SCS; 2) The abundance of MP in the benthic nektons (0.52 ± 0.24 items individual-1) was higher than that in the pelagic nektons (0.30 ± 0.11 items individual-1). Accordingly, the mean hazard score of MPs detected in the benthic nektons (220.66 ± 210.75) was higher than that in the pelagic nektons (49.53 ± 22.87); 3) The mean size of the MP in the pelagic nektons (0.84 ± 0.17 mm) was larger than that in the benthic nektons (0.49 ± 0.09 mm). Our findings highlight the need to further investigate the ecological impacts of MPs on wild nekton, especially commercially important species, and its potential implications for human health.

Microplastics in three typical benthic species from the Arctic: Occurrence, characteristics, sources, and environmental implications.

Microplastics (MPs) in the Arctic have raised increasing concern, but knowledge on MP contamination in benthic organisms from Arctic shelf regions, e.g., the Chukchi Sea is still limited. Therefore, the present study investigated the occurrence, characteristics, sources, and environmental implications of MPs in the three most common benthic species, namely sea anemone (Actiniidae und.), deposit-feeding starfish (Ctenodiscus crispatus), and snow crab (Chionoecetes opilio), from the Chukchi Sea. The abundances of MPs in the three benthic species were significantly greater than those from the Bering Sea, but lower than those from other regions globally. The top three compositions of MPs in the three species were polyester, nylon, and polyethylene terephthalate. The detection limit for MP size in the present study was 0.03 mm and the mean size of MP in the three species was 0.89 ± 0.06 mm. The surfaces of MPs found in the starfish and crabs were covered with many attachments, cracks, and hollows, while the surfaces of MPs found in the sea anemones were smooth, which was likely a consequence of different feeding behaviors. There was a significantly positive correlation between the abundances of MPs and other anthropogenic substances. The mean MP abundances in the sea anemones ranged from 0.2 items/individual to 1.7 items/individual, which was significantly higher than that in the deposit-feeding starfish (0.1-1.4 items/individual) and snow crabs (0.0-0.6 items/individual). Sea anemones inhabiting lower latitudes ingested relatively higher levels of MPs than those inhabiting higher latitudes. The MP abundances in the sea anemones are significantly and positively correlated with the seasonal reduced ratio of sea ice coverage from August to September. Our findings indicate that sea anemones could function as a bioindicator of MP pollution, and that the MPs in the benthos from the Chukchi Sea might originate from the melting sea ice, fishery activities and ocean currents.

Reidentification of Decapterus macarellus and D. macrosoma (Carangidae) reveals inconsistencies with current morphological taxonomy in China.

Decapterus macarellus and D. macrosoma are economically important pelagic fish species that are widely distributed in tropical and subtropical seas. The two species are often mistakenly identified due to their morphological similarities as described in the Chinese literature on fish identification. In this study, D. macarellus and D. macrosoma samples were collected in the Eastern Indian Ocean and the South China Sea and reidentified using morphological and DNA barcoding techniques. The characteristics that distinguish the two species primarily include the scute coverage of the straight portion of the lateral line (the most indicative characteristic for classification), the shape of the predorsal scaled area and its location relative to the middle axis of the eye, and the shapes of the posterior margin of the maxilla and the posterior margin of the operculum. The results revealed a large number of misidentified sequences among the homologous cytochrome oxidase (COI) sequences of the two species in the NCBI database and that the genus Decapterus may include cryptic species. In terms of genetic structure, the Sundaland has not blocked genetic exchange between D. macarellus populations in the South China Sea and the Eastern Indian Ocean, giving rise to a high level of genetic diversity. In this study, we made corrections to the Chinese classification standards for D. macarellus and D. macrosoma and the erroneous reference sequences in the NCBI database, thereby providing accurate reference points for the future exploration of cryptic species in the genus Decapterus.

Pleistocene isolation caused by sea-level fluctuations shaped genetic characterization of Pampus minor over a large-scale geographical distribution.

The southern lesser pomfret (Pampus minor) is an economically important fish, and its numbers are declining because of overfishing and environmental pollution. In addition, owing to the similarities of its external morphological characteristics to other species in the genus Pampus, it is often mistaken for grey pomfret (P. cinereus) or silver pomfret (P. argenteus) juveniles. In this study, the genetic diversity and structure of 264 P. minor individuals from 11 populations in China and Malaysia coastal waters were evaluated for the first time, to the best of our knowledge, using mitochondrial cytochrome b fragments. The results showed that P. minor had moderate haplotype diversity and low nucleotide diversity. Furthermore, two divergent lineages were detected within the populations, but the phylogenetic structure corresponded imperfectly with geographical location; thus, the populations may have diverged in different glacial refugia during the Pleistocene low sea levels. Analysis of molecular variation (AMOVA) showed that genetic variation originated primarily from individuals within the population. Pairwise F ST results showed significant differentiation between the Chinese and Malaysian populations. Except for the Xiamen population, which was classified as a marginal population, the genetic differentiation among the other Chinese populations was not significant. During the Late Pleistocene, P. minor experienced a population expansion event starting from the South China Sea refugium that expanded outward, and derivative populations quickly occupied and adapted to the new habitat. The results of this study will provide genetic information for the scientific conservation and management of P. minor resources.

Effects of Different Salt Concentrations on Several Freshness Indicators of North Pacific Squid (Ommastrephes sloani pacificus) during Storage at 4°C.

ABSTRACT: The effects of salt treatment (2% [w/w] low salt and 6% [w/w] high salt) and storage time (0 to 12 days) on two biogenic amines (histamine and tyramine), total volatile base nitrogen (TVB-N), pH, and volatile compounds of the North Pacific squid during storage at 4°C were evaluated. The freshness of squid muscle was evaluated by monitoring the changes in these indicators during storage. Results showed that histamine and tyramine contents increased with storage time (4.29 to 22.47 mg/kg for histamine and 28.10 to 135.78 mg/kg for tyramine) and that, in samples treated with salt, formation of these amines can be effectively inhibited (P < 0.05) compared with untreated samples. The overall pH level initially decreased and then increased during storage (ranging from 6.49 to 7.13), and the pH level of the two salt treatment groups was a little lower than that of the control group. The TVB-N value increased with time and was effectively inhibited by salt (P < 0.05). The number and content of the volatile components in squid varied during the entire storage time. The main volatile components detected in North Pacific squid were aliphatic hydrocarbons, alcohols, aldehydes, ketones, acids, esters, aromatic hydrocarbons, phenols, nitrogenous compounds, sulfo compounds, and esters. Several compounds, such as trimethylamine, butyric acid, and sulfureted hydrogen, can be used to determine the quality of aquatic products, and salt treatment can inhibit their formation. The TVB-N value was significantly correlated with pH level and with the concentrations of histamine, tyramine, and several volatile compounds in all samples (P < 0.05). In summary, salt concentration had a positive effect on extending the shelf life of North Pacific squid, and multiple indicators should be used to determine the quality of squid.

The antibacterial activity and mechanism analysis of piscidin 5 like from Larimichthys crocea.

Chemical drugs, such as antibiotics, were still important materials to prevent and cure diseases of aquatic organisms. However, antibiotics abuse do not only make the effects little, but also cause other bad problems, such as bacterial resistance and drug residues. Therefore, seeking the effective substitutes of antibiotics was an approach needed to be explored. Antibacterial peptides (AMPs) attracted more and more attention in the recent years. The parasitism and secondary bacterial invasion caused by ectroparasite Cryptocaryon irritans was a disaster to almost all host fish, including Larimichthys crocea. Reports indicated many AMPs played a key role in the whole parasitic infection cycle. Piscidin 5 like was a member of piscidin family. In the study, the antibacterial activity and mechanisms of piscidin 5 like from L.coreca (Lc-P5L) were detected. Liquid growth inhibition results showed recombinant Lc-P5L (rLc-P5L) had broad antibacterial spectrum and strong bactericidal activity. The bactericidal activity functioned in dose- and time-dependent manners. SEM (scanning electron microscope) observed the relatively detailed bactericidal process, rLc-P5L treatment resulted in a mass of bacteria piling together, appearing plenty of strange filaments and covering on the bacteria. Besides, S.aureus overgrowed plenty of granules, formed holes on the membrane of a few cells, and contents poured out from the holes. At the same time, antibacterial mechanisms were explored. After direct incubation with bacteria, western blot detected the apparently positive signal of rLc-P5L on bacteria; secondly, the incubation first with LPS (lipopolysaccharide) or LTA (lipoteichoic acid) significantly affect the binding of rLc-P5L to bacteria again, which indicated rLc-P5L could bind to bacteria through interaction with some PAMPs (pathogen-associated molecular patterns). In addition, rLc-P5L could interact with bacterial genome DNA by dose- and time-dependent means. In summary, rLc-P5L binded to bacteria surface through targeting to some PAMPs to damage membrane, and entered into cells to interact with genome DNA to disturb normal metabolism when it reached to some certain time and concentration thresholds, which were likely to be its pathway to exert antibacterial activity.

Complete mitochondrial genome sequence and phylogenetic analysis of Lycodes polaris (Sabine, 1824).

Lycodes polaris is one of the most widely distributed and abundant eelpout species on the Arctic continental shelves with full mitogenome information unavailable. In this paper, complete mitochondrial genome of L. Polaris was determined with 16,595 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and 2 non-coding regions (origin of light strand replication and control region). All the protein-coding genes choose ATG as start codon in addition to that COI using GTG. Most genes use TAA or TAG as the stop codon while three others ended with incomplete stop codons. Phylogenetic relationship of L. polaris was also reconstructed. Our result will provide important basis for further studies of L. polaris.

Microplastic contamination in benthic organisms from the Arctic and sub-Arctic regions.

The seafloor is recognized as one of the major sinks for microplastics (MPs). However, to date there have been no studies reported the MP contamination in benthic organisms from the Arctic and sub-Arctic regions. Therefore, this study provided the first data on the abundances and characteristics of MPs in a total of 413 dominant benthic organisms representing 11 different species inhabiting in the shelf of Bering and Chukchi Seas. The mean abundances of MP uptake by the benthos from all sites ranged from 0.02 to 0.46 items g-1 wet weight (ww) or 0.04-1.67 items individual-1, which were lower values than those found in other regions worldwide. The highest value appeared at the northernmost site, implying that the sea ice and the cold current represent possible transport mediums. Interestingly, the predator A. rubens ingested the maximum quantities of MPs, suggesting that the trophic transfer of MPs through benthic food webs may play a critical role. Fibers constituted the major type (87%) in each species, followed by film (13%). The colors of fibers were classified as red (46%) and transparent (41%), and the film was all gray. The predominant composition was polyamide (PA) (46%), followed by polyethylene (PE) (23%), polyester (PET) (18%) and cellophane (CP) (13%). The most common sizes of MPs concentrated in the interval from 0.10 to 1.50 mm, and the mean size was 1.45 ±â€¯0.13 mm. Further studies about the temporal trends and detrimental effects of MPs remain to be carried out in benthic organisms from the Arctic and sub-Arctic regions.

New identification of the moray eel Gymnothorax minor (Temminck & Schlegel, 1846) in China (Anguilliformes, Muraenidae).

A new identification of Gymnothorax minor (Temminck & Schlegel, 1846) is documented based on morphological characteristics and DNA barcoding. Sixty-one individuals of G. minor were collected from the East China Sea and the South China Sea. This species was previously reported as Gymnothorax reticularis Bloch, 1795 in China because of the similarity in external shape and color. Gymnothorax minor can be easily distinguished from G. reticularis by its color pattern of 18-20 irregular dark brown vertical bars and the body having scattered small brown spots. Additionally, the teeth are uniserial on both jaws, and the vertebrae number 137-139. By combining congener sequences of the cytochrome oxidase I (COI) gene from GenBank, two groups were detected among all the COI sequences of the currently named G. minor, which further indicated that two valid species were present based on genetic distance. A divergence also occurred on the number of vertebrae between the northern and southern populations. The phylogenetic and morphological analysis strongly supports that the northern and southern populations of G. minor are two different species. Furthermore, the distribution area of the northern G. minor has expanded southward to 5°15'N in the South China Sea. More specimens of G. minor and G. reticularis are crucial in order to define their geographical distribution boundaries and provide the correct DNA barcoding.

Genetic signatures of polymorphic microsatellite loci in the Ambiguous silver pomfret, Pampusargenteus (Teleostei, Stromateidae).

Pampusargenteus is a broadly exploited pelagic fish species, commonly misidentified as Pampusechinogaster. Genetic variation and population structure in Pampusargenteus was studied based on seven microsatellite loci. The observed high average allele number, heterozygosity values, and polymorphism information content of P.argenteus suggested high genetic diversity. No population genetic differentiation was detected based on the results of pairwise F st, three-dimensional factorial correspondence analysis (3D-FCA) and STRUCTURE analysis, which implied continuous gene flow. Wilcoxon signed rank tests did not indicate significant heterozygosity excess, and recent genetic bottleneck events were not detected. Coupled with previous mitochondrial DNA results, the findings presented here indicate that high gene flow characterizes the current phylogeographic pattern of the species.

Radioactive impacts on nekton species in the Northwest Pacific and humans more than one year after the Fukushima nuclear accident.

This study investigated the radioactive impacts on 10 nekton species in the Northwest Pacific more than one year after the Fukushima Nuclear Accident (FNA) from the two perspectives of contamination and harm. Squids were especially used for the spatial and temporal comparisons to demonstrate the impacts from the FNA. The radiation doses to nekton species and humans were assessed to link this radioactivity contamination to possible harm. The total dose rates to nektons were lower than the ERICA ecosystem screening benchmark of 10µGy/h. Further dose-contribution analysis showed that the internal doses from the naturally occurring nuclide 210Po were the main dose contributor. The dose rates from 134Cs, 137Cs, 90Sr and 110mAg were approximately three or four orders of magnitude lower than those from naturally occurring radionuclides. The 210Po-derived dose was also the main contributor of the total human dose from immersion in the seawater and the ingestion of nekton species. The human doses from anthropogenic radionuclides were ~ 100 to ~ 10,000 times lower than the doses from naturally occurring radionuclides. A morbidity assessment was performed based on the Linear No Threshold assumptions of exposure and showed 7 additional cancer cases per 100,000,000 similarly exposed people. Taken together, there is no need for concern regarding the radioactive harm in the open ocean area of the Northwest Pacific.

New genetic perspectives of the ambiguous pomfret as revealed by CR sequences.

Pampus argenteus is an economically important fish that is often erroneously identified as Pampus echinogaster. No population genetic analyses have been performed on the true P. argenteus species. Here, the mitochondrial control region (CR) was used to evaluate the population genetics and elaborate the historical demography of the Silver pomfret collected from six geographical locations in China, Pakistan, and Kuwait. A high level of genetic diversity was demonstrated in this species. Analysis of molecular variance (AMOVA) revealed that the genetic divergence was mainly derived from within the populations (P < 0.05). A historical demographic analysis indicated that the Silver pomfret experienced a recent population expansion during the late Pleistocene. The phylogeographical structure revealed two obvious lineages that diverged in the late Pleistocene, during which the Silver pomfret populations historically experienced exotic divergence and mixed again with differentiated populations. Currently, Silver pomfret populations have insufficient time to attain migration-drift equilibrium. Population genetic data of the Silver pomfret can provide preliminary genetic knowledge for its fishery management.

The complete mitochondrial genome of the tessellated leatherjacket Thamnaconus tessellatus (Tetraodontiformes: Monacanthidae).

The long PCR and primer walking methods were applied for obtaining the complete mitochondrial genome of the tessellated leatherjacket Thamnaconus tessellatus. The complete mitochondrial genome was 16,437 bp in length and contained 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, an origin of L-strand replication and a control region. The arrangements and characteristics of these segments shared common features with other teleosts. Extended termination associated sequence domain (TAS, cTAS), central conserved sequence block domain (CSB-F, CSB-E, CSB-D) and conserved sequence block domain (CSB-1, CSB-2, CSB-3) were identified in the control region.

The complete mitochondrial genome of Pampus echinogaster (Perciformes: Stromateidae).

The long PCR and primer walking methods are employed for determining the complete mitochondrial genome sequence of Pampus echinogaster. The mitogenome is a circular molecule of 17,694 bp in length including the structure of 13 protein-coding genes, 2 ribosomal RNA genes, 23 transfer RNA genes and 2 non-coding regions (L-strand replication origin and control region). Two tRNA(Met) genes are identified in the tRNA-IQM region. Within the control region, we identify the termination-associated sequence domain (TAS), a central conserved domain (CSB-F, CSB-E and CSB-D) and three conserved sequence blocks (CSB-1, CSB-2 and CSB-3). There are 10 copies of tandem repeats of 120-124 bp in the control region, which contain CSB-3.

Genetic differentiation of Trachurus japonicus from the Northwestern Pacific based on the mitochondrial DNA control region.

Trachurus japonicus is a pelagic fish widely distributed from China, Korea to Japan. To examine the gene flow of T. japonicus between Chinese and Japanese coastal waters, eight populations were collected for the present study. Eighty-seven variable sites defined 168 haplotypes. The populations of T. japonicus showed high haplotype diversity (h) with a range from 0.964 ± 0.027 to 1.000 ± 0.016 and low nucleotide diversity with a range from 0.011 ± 0.006 to 0.015 ± 0.008. The topology of the neighbour-joining tree showed no significant genealogical branches or clusters corresponding to sampling localities. The starburst structure of the minimum spanning tree suggested a very recent origin for most haplotypes. Both pairwise F st and analysis of molecular variance revealed no significant genetic differentiation throughout the range examined. The results of neutrality tests and mismatch distributions indicated that T. japonicus may experience a recent population demographic expansion.