Genetic identification of two species of Pleuronichthys by DNA barcoding

DNA barcoding is a new method for biological taxonomy, offering the ability to identify species from fragments in any life-history stage. Pleuronichthys cornutus and P. japonicus are two morphologically similar species. Pleuronichthys japonicus has never been found previously in China. However, in this study, we identified both species using DNA barcoding (cytochrome c oxidase subunit I (COI)), the mtDNA control region and cytochrome b. The results reveal that: 1) intraspecific variation in the DNA barcode ...     

Phytoplankton abundance and community structure in the Antarctic polar frontal region during austral summer of 2009

The Antarctic polar front region in the Southern Ocean is known to be most productive. We studied the phytoplankton community structure in the Indian sector at this frontal location during late austral summer (February, 2009) onboard R/V Akademic Boris Petrov. We used the phytoplankton and microheterotrophs abundance, as also the associated physico-chemical parameters to explain the low phytoplankton abundance in the study region. This study emphasizes the shift of phytoplankton, from large (>10 μm) to small (<10 μm) size. The phytoplankton abundance appears to be controlled by physical parameters and by nutrient concentrations and also by the microheterotrophs (ciliates and dinoflagellates) which exert a strong grazing pressure. This probably reduces small (<10 μm) and large (>10 μm) phytoplankton abundance during the late austral summer. This study highlights the highly productive polar front nevertheless becomes a region of low phytoplankton abundance, due to community shifts towards pico-phytoplankton (<10 μm) during late austral summer.     

Features and spatial distribution of circumpolar deep water in the southern Indian Ocean and the effects of Antarctic circum polar current

The data from the Southern Ocean observations of World Ocean Circulation Experiment(WOCE) are used for analysis and illustration of the features and spatial distributions of Circumpolar Deep Water(CDW) in the southern Indian Ocean.It is learnt from the comparison among the vertical distributions of temperature/salinity/oxygen along the 30°E,90°E and 145°E sections respectively that some different features of CDW and the fronts can be found at those longitudes,and those differences can be attributed to the zonal transoceanic flow and the merizonal movement in the Circumpolar Deep Water.In fact,the zonal transoceanic flow is the main dynamic factor for the water exchange between the Pacific Ocean and the Indian Ocean or between the Atlantic Ocean and the Indian Ocean,and for the effects on the spatial distributions of the physical properties in CDW.     

Evaluation of reanalysis and satellite-based sea surface winds using in situ measurements from Chinese Antarctic Expeditions

Sea surface winds from reanalysis （NCEP-2 and ERA-40 datasets） and satellite-based products （QuikSCAT and NCDC blended sea winds） are evaluated using in situ ship measurements from the Chinese National Antarctic Research Expeditions （CH1NAREs） from 1989 through 2006, with emphasis on the Southern Ocean （south of 45°S）. Compared with ship observations, the reanalysis winds have a positive mean bias （0.32 m·s-1 for NCEP-2 and 0.13 m·s-1 for ERA-40）, and this bias is more pronounced in the Southern Ocean （0.57 m·s-1 and 0.45 m·s-1, respectively）. However, mean biases are negative in the tropics and subtropics. The satellite-based winds also show positive mean biases, larger than those of the reanalysis data. All four wind products overestimate ship wind speed for weak winds （〈4 m·s-1） but underestimate for strong winds （〉10 m·s-1）. Differences between the reanalysis and satellite winds are examined to identify regions with large discrepancies.     

3种柔鱼线粒体基因与核核糖体基因片段序列比较分析

为准确检测柔鱼（Ommαstrephesbartram川、茎柔鱼（ Dosidicus gigas）与阿根廷滑柔鱼（ IIIex argentinus ） 的种间遗传差异,对线粒体16SrRNA、细胞色素b（Cytb）与编码核糖体大亚基的基因（28SrDNA）片段序列进 行测定。经比对获得同源片段序列的长度分别为444、430、464坤,其中16SrRNA与28SrDNA基因片段上分别存在3处和47处碱基插入/缺失。核昔酸组成分析表明;3种柔鱼在3个基因片段上的核音酸组成差异不显著, 在线粒体2个基因片段上的A＋T含量（16SrRNA;69.90%、72.01%、74.66%; Cytb; 63.61%、68.91%、71.65% ） 均明显高于C＋C含量（16SrRNA;30.10%、27.99%、25.34%; Cytb; 36.39%、31.09%、28.35% ）,而在28SrDNA 基因片段上的A＋T含量（37.16%、36.74%、38.29% ）明显低于C＋C含量（62.84%、63.26%、61.71 %）0 3种柔鱼 在28SrDNA基因片段上检测到的核昔酸替代率最低,为6.68%,而蛋白质编码基因Cytb核昔酸替代率最高,为 20.93%,核营酸替代均发生在密码子第3位点上,而且未引起氨基酸替代。基于邻接法、最大简约法与最大似然 法重建的系统树显示,柔鱼与茎柔鱼的亲缘关系较近。根据C严b基因片段序列分析,柔鱼与茎柔鱼和阿根廷滑柔鱼的分歧时间分别为653-790万a和765 - 925万a,种间分化事件发生在中新世至上新世间。     

Application of otolith shape analysis for stock discrimination and species identification of five goby species （Perciformes： Gobiidae） in the northern Chinese coastal waters

We tested the use of otolith shape analysis to discriminate between species and stocks of five goby species( Ctenotrypauchen chinensis, Odontamblyopus lacepedii, Amblychaeturichthys hexanema, Chaeturichthys stigmatias, and Acanthogobius hasta) found in northern Chinese coastal waters. The five species were well differentiated with high overall classification success using shape indices(83.7%), elliptic Fourier coefficients(98.6%), or the combination of both methods(94.9%). However, shape analysis alone was only moderately successful at discriminating among the four stocks(Liaodong Bay, LD; Bohai Bay, BH; Huanghe(Yellow) River estuary HRE, and Jiaozhou Bay, JZ stocks) of A. hasta(50%–54%) and C. stigmatias(65.7%–75.8%). For these two species, shape analysis was moderately successful at discriminating the HRE or JZ stocks from other stocks, but failed to effectively identify the LD and BH stocks. A large number of otoliths were misclassified between the HRE and JZ stocks, which are geographically well separated. The classification success for stock discrimination was higher using elliptic Fourier coefficients alone(70.2%) or in combination with shape indices(75.8%) than using only shape indices(65.7%) in C. stigmatias whereas there was little difference among the three methods for A. hasta. Our results supported the common belief that otolith shape analysis is generally more effective for interspecific identification than intraspecific discrimination. Moreover, compared with shape indices analysis, Fourier analysis improves classification success during inter- and intra-species discrimination by otolith shape analysis, although this did not necessarily always occur in all fish species.     

A preliminary study on the diversity of fish species and marine fish faunas of the South China Sea

There are 3048 species offish occurring in the China Seas (CS), of which at least 2321 species are found in the South China Sea (SCS), belonging to 35 orders, 236 families and 822 genera. The fish species diversity is analyzed in this paper based on biogeography, biostatisties, fishing methods, etc. It is found that the regional environment, especially biological factors, plays an important role in the distribution of faunas, and there are two fish faunas in the SCS, one in the north and another in the center and south. This regional division is of value for sustainable fishery production and efficient management of fishery resources.     

Effects of heavy metal ions (Cu2+, Pb2+ and Cd2+) on DNA damage of the gills, hemocytes and hepatopancreas of marine crab, Charybdis japonica

There are rising concerns about the hazardous effects of heavy metals on the environment. In this study, comet assay and DNA alkaline unwinding assay were conducted on the tissues (gills, hepatopancreas, and hemocytes) of Charybdis japonica in order to illustrate genotoxicity of three heavy metal ions (Cu2+, Pb2+, and Cd2+) on the marine crabs C. japonica. The crabs were exposed to Cu2+ (10, 50, and 100 ?g.L?1), Pb2+ (50, 250, and 500 ?g L?1) and Cd2+ (5, 25, and 50 ?g L?1), and the tissues were sampled at days 0.5, 1, 3, 6, 9, and 15. DNA alkaline unwinding assay was used for testing the DNA single strand break in gills and hepatopancreas and comet assay was employed for testing the DNA damage in hemocytes. The results showed that the DNA damage (F-value) of gills in the crabs exposed to the three heavy metals was decreased gradually during the exposure periods and there was a dose-time response relationship in certain time, suggesting that the levels of DNA single strand break in all the experimental groups increased significantly compared to the controls. Changes of F-value in hepatopancreas of the crabs exposed to the three heavy metals were similar to those in gills except that the peak values were found in the 500 ?g L?1 Pb2+ treatment group at day 3 and the 50 ?g L?1 Cd2+ treatment group at day 9. The ranks of DNA damage in gills and hepatopancreas induced by the three heavy metal ions (50 ?g L?1, day 15) were Cd2+ >Pb2+ >Cu2+ and Pb2+ >Cu2+ >Cd2+. The levels of DNA damage in gills were higher than those in hepatopancreas in the same experimental group. It can be concluded that indices of DNA damage can be used as the potential biomarkers of heavy metal pollution in marine environment.     

Use of Otolith Shape for the Identification of Trumpeter Sillago （Sillago maculata） and Silver Sillago （Sillago sihama）

Otolith shape is species-specific in fish. In this study, 161 samples of Trumpeter sillago Sillago maculata and 164 of Silver sillago Sillago sihama were collected from Beibu Gulf in July 2009. The main objective of this study was to use morphological variables and Fourier harmonics to describe otolith characteristics and use discriminant analyses to separate the two species. Otoliths were measured by traditional one and two dimensional measures(otolith length, width, diameters, area, perimeter, rectangularity and circularity), as well as by Fourier analysis to capture the finer regions of the otolith. Analysis of covariance(ANCOVA)showed that there was significant correlation between morphological variables(diameter, perimeter, otolith length, otolith width, otolith area, density, harmonics 3, harmonics 4, harmonics 5, harmonics 13, harmonics 15, and harmonics 16)and body length. To minimize size effects on the morphological variables between species, only fish with a body length between 90 and 140 mm were included in the data analysis and the variables which had significant relation with body length were transformed using the residual. The result showed that the accuracy of discriminant analysis was 97. 8% and 100% for Trumpeter sillago and Silver sillago, respectively. This high accuracy indicated that otolith shape was described accurately by morphological variables and Fourier harmonics, and discriminant analysis was an effective way to identify and separate the two species.