Population genetic structure of the mantis shrimp Oratosquilla oratoria(Crustacea: Squillidae) in the Yellow Sea and East China Sea

The mantis shrimp O ratosquilla oratoria is an ecologically and economically important species in the Western Pacific. In present study, the population genetic structure of O ratosquilla oratoria from the Yellow Sea and East China Sea was examined with mitochondrial DNA control region sequences. In total, 394 samples were collected from 18 locations and 102 haplotypes were obtained. For the Yellow Sea, the overall nucleotide diversity and haplotype diversity were 0.006 9 and 0.946 8, respectively; while across all the East China Sea locations, the overall nucleotide diversity and haplotype diversity were 0.027 94 and 0.979 0, respectively. The results of AMOVA and pairwise F_(ST)(0.145 2, P 0.001) revealed moderate differentiation between the Yellow Sea and East China Sea populations of O. oratoria. However, neither the neighbor-joining tree nor haplotype network showed clades with geographic pattern, which indicated considerable gene flow was existed between the Yellow Sea and East China Sea, and supporting the high larval dispersal ability in this species. Mismatch distribution analysis and neutrality tests suggested that O. oratoria has undergone population expansion event, and the Pleistocene glacial cycles might have an impact on the historical demography of O. oratoria. The genetic information obtained in this study can provide useful information for sustainable improvements for capture fisheries management strategies.     

Mitochondrial DNA control region diversity and population structure of Pacific herring (Clupea pallasii) in the Yellow Sea and the Sea of Japan

To investigate the genetic variation and population structure of Pacific herring in the Yellow Sea and the genetic differentiation between the Yellow Sea and the Sea of Japan,fragments of 479-bp mitochondrial DNA control region were sequenced for 110 individuals collected from three different periods in the Yellow Sea and one locality in the Sea of Japan.High haplotype diversity and moderate nucleotide diversity were observed in Pacific herring.AMOVA and exact test of population differentiation showed no significant genetic differentiations among the three populations of the Yellow Sea and suggested the populations can be treated as a single panmictic stock in the Yellow Sea.However,a large and significant genetic differentiation(WST50.11;P50.00) was detected between the populations in the Yellow Sea and the Sea of Japan.The high sea water temperature in the Tsushima Strait was thought a barrier to block the gene exchange between populations of the two sea areas.The neutrality tests and mismatch distribution indicated recent population expansion in Pacific herring.     

3种星虫线粒体16S rRNA、COI和Cyt b基因片段的序列比较

对裸体方格星虫(Sipunculus nudus)、可口革囊星虫(Phascolosoma esculenta)和澳洲管体星虫(Siphonosoma australe)的线粒体16S rRNA、COI和细胞色素b(Cytb)基因片段序列进行比较,并对其系统发生进行了初步探讨。采用PCR方法得到总长度分别为531～544bp(16S)、652～675bp(COI)和406～453bp(Cytb)的线粒体片段。片段碱基A+T比例较高(16S rRNA基因58.3%,COI基因56.9%,Cytb基因59.5%)。16S rRNA片段存在169个碱基变异位点(其中包括167个简约信息位点)和44个碱基插入/缺失,种内个体间变异较小;COI片段有512个碱基(333个简约信息位点)存在变异,79个碱基插入/缺失;Cytb片段存在347个碱基(318个简约信息位点)变异位点,16个碱基插入/缺失。数据分析结果支持3种星虫和环节动物的分类地位较近,与软体动物较远的分类观点。此外,裸体方格星虫与澳洲管体星虫之间亲缘关系较近(D=0.3159、0.3156、0.2361)。认为3种星虫线粒体16S rRNA、COI和Cytb基因在种间存在明显的多态性,证实了三种基因序列均普遍适用于星虫种及以上阶元的系统学分析。     

钦州湾牡蛎线粒体16S rRNA和COⅠ基因片段的序列变异分析

利用线粒体16S rRNA基因和线粒体细胞色素氧化酶亚基Ⅰ(cytochrome oxidaseⅠ,COⅠ)基因片段初步研究钦州湾牡蛎(Ostrea)的物种组成。以特异引物进行PCR扩增,对扩增产物进行纯化、测序,分析表明,16S rRNA基因部分长度为413bp,COⅠ基因部分长度为535bp,2种牡蛎序列的碱基组成均显示出较高的A+T比例:16S rRNA基因59.8%;COⅠ基因60.5%。对位排序比较表明,16S rRNA片段种内个体间变异较小,存在7个变异位点,4种单倍型,其中包括5个转换位点突变,2个颠换位点突变;COⅠ片段有30个碱基存在变异,7种单倍型,其中包括16个转换位点突变,14个颠换位点突变。运用MEGA4软件计算出不同个体间的遗传距离,并构建了NJ和UPGMA系统树。香港牡蛎(Crassostrea hongkongensis)16S rRNA和COⅠ序列与白肉牡蛎的遗传距离均为0.000,有明巨牡蛎(Crassostrea ariakensis)16S rRNA和COⅠ序列和红肉牡蛎(red meat ostrea)的遗传距离分别为0.000和0.011,白肉牡蛎16S rRNA和COⅠ序列和红肉牡蛎之间的遗传距离分别为0.035和0.146。结果表明,钦州湾牡蛎分为2个不同的种,线粒体16S rRNA和COⅠ基因在种间存在明显的多态性,证实了16S rRNA和COⅠ基因序列适用于牡蛎的系统学分析。     

钦州湾牡蛎线粒体16SrRNA和COI基因片段的序列变异分析

利用线粒体16SrRNA基因和线粒体细胞色素氧化酶亚基Ⅰ（cvtocllrome oxidase Ⅰ，COI）基因片段初步研究钦州湾牡蛎（Ostxea）的物种组成。以特异引物进行PCR扩增，对扩增产物进行纯化、测序，分析表明，16SrRNA基因部分长度为413bp，COI基因部分长度为535bp，2种牡蛎序列的碱基组成均显示出较高的A＋T比例：16SrRNA基因598％；COI基因605％。对位排序比较表明，16SrRNA片段种内个体间变异较小，存在7个变异位点，4种单倍型，其中包括5个转换位点突变，2个颠换位点突变；COI片段有30个碱基存在变异，7种单倍型，其中包括16个转换位点突变，14个颠换位点突变。运用MEGA4软件计算出不同个体间的遗传距离，并构建了NJ和UPGMA系统树。香港牡蛎（Crassostrea hongkongensis）16SrRNA和COI序列与白肉牡蛎的遗传距离均为0000，有明巨牡蛎（Crassostrea ariakensis）16SrRNA和COI序列和红肉牡蛎（redmeatostxea）的遗传距离分别为0000和0011，白肉牡蛎16SrRNA和COI序列和红肉牡蛎之间的遗传距离分别为0035和0146。结果表明，钦州湾牡蛎分为2个不同的种，线粒体16SrRNA和COI基因在种间存在明显的多态性，证实了16SrRNA和COI基因序列适用于牡蛎的系统学分析。     

A New Molecular Label Applied to the Study of the Yellow Sea Green Tide

From 2007 to 2017, large-scale green tides occurred every year in the Yellow Sea of China, and Ulva prolifera was the main species leading to the green tide. In this study, we used the Polymerase chain reaction and 3' Rapid-amplification of c DNA ends technique to amplify the nr DNA-LSU and IGS sequences in U. prolifera and one species of Blidingia. These techniques showed 3259 bp of nrD NA-LSU and 3388 bp of IGS in U. prolifera and 3282 bp nr DNA-LSU and 3059 bp IGS in Blidingia sp. At the same time, tandem repeats, short dyads, palindromic and multiple simple repeat sequences in the IGS sequence were found by analyzing the structure of the IGS sequence in U. prolifera and Blidingia sp. G + C contents of the IGS sequence in U. prolifera and Blidingia sp. were 52.42% and 53.09%, respectively. We divided the U. prolifera into two types according to the morphological characteristics. Although the specimens of U. prolifera from the Qingdao coastal area, Jiangsu coastal area and the Yellow Sea have different morphologies, their ITS and IGS sequences are almost identical. Therefore, the main species of the green tides in the Qingdao coastal area, Jiangsu coastal area and the Yellow Sea are the same and have the same origin.     

Genetic diversity in two Japanese flounder populations from China seas inferred using microsatellite markers and COI sequences

Japanese flounder is one of the most important commercial species in China; however, information on the genetic background of natural populations in China seas is scarce. The lack of genetic data has hampered fishery management and aquaculture development programs for this species. In the present study, we have analyzed the genetic diversity in natural populations of Japanese flounder sampled from the Yellow Sea (Qingdao population, QD) and East China Sea (Zhoushan population, ZS) using 10 polymorphic microsatellite loci and cytochrome c oxidase subunit I (COI) sequencing data. A total of 68 different alleles were observed over 10 microsatellite loci. The total number of alleles per locus ranged from 2 to 9, and the number of genotypes per locus ranged from 3 to 45. The observed heterozygosity and expected heterozygosity in QD were 0.733 and 0.779, respectively, and in ZS the heterozygosity values were 0.708 and 0.783, respectively. Significant departures from Hardy-Weinberg equilibrium were observed in 7 of the 10 microsatellite loci in each of the two populations. The COI sequencing analysis revealed 25 polymorphic sites and 15 haplotypes in the two populations. The haplotype diversity and nucleotide diversity in the QD population were 0.746±0.072 8 and 0.003 34±0.001 03 respectively, and in ZS population the genetic diversity values were 0.712±0.047 0 and 0.003 18±0.000 49, respectively. The microsatellite data (F_st =0.048 7, P<0.001) and mitochondrial DNA data (F_st =0.128, P<0.001) both revealed significant genetic differentiation between the two populations. The information on the genetic variation and differentiation in Japanese flounder obtained in this study could be used to set up suitable guidelines for the management and conservation of this species, as well as for managing artificial selection programs. In future studies, more geographically diverse stocks should be used to obtain a deeper understanding of the population structure of Japanese flounder in the China seas and adjacent regions.     

湛江海域文昌鱼(Branchiostoma)线粒体Cyt b基因的全序列分析

测定了邻近湛江的茂名海区和硇洲岛海域文昌鱼各2个样本线粒体Cytb基因全序列,以尾索动物亚门的2种海鞘(Ciona spp.)和脊椎动物亚门的七鳃鳗(Petromyzon marinus)作为外群,利用分子系统学方法与GenBank收录的14个文昌鱼(Branchiostoma)的Cytb基因全序列进行了比较,UPGMA法构建了系统发生树。全序列分析表明:主产于大西洋(批针文昌鱼B.lanceolatum和佛罗里达文昌鱼B.floridae)、厦门文昌鱼(B.belcheri belcheri Gray)和湛江文昌鱼线粒体Cytb基因全序列长度为1143bp,终止密码子同为UAG;主产于青岛文昌鱼(B.belcheri tsingtaunese)和日本文昌鱼为1141bp,以T结尾,转录过程中构成UAA终止密码子。系统分析表明:16个文昌鱼样品体现出太平洋和大西洋、太平洋南北明显分化。确认采自茂名和硇洲岛的文昌鱼为厦门文昌鱼(B.belcheribelcheriGray);支持将白氏文昌鱼青岛亚种(B.belcheri tsingtaunese)提升为种,命名为日本文昌鱼(B.japonicus)。     

星洲银罗非鱼线粒体细胞色素b基因的序列分析

克隆并测定了星洲银罗非鱼(Oreochromis sp.)细胞色素b基因(cyt b)的全序列,得到全长1 141bp的序列用于分析,用MEGA4.0分析软件与GenBank中的线粒体DNA序列进行序列比较,显示星洲银罗非鱼与其他鱼类的cyt b基因的同源性较高,同源度介于83%~93%间;根据星洲银罗非鱼与莫桑比克罗非鱼、尼罗罗非鱼等12种鱼类的cyt b基因序列构建的系统进化树,初步确定尼罗罗非鱼、莫桑比克罗非鱼为星洲银罗非鱼的父母本。     

Are Acila divaricata and Acila mirabilis One Species or Two Distinct Species?Evidence from COI Mitochondrial DNA

Acila divaricata (Hinds, 1843) and A. mirabilis (Adams and Reeve, 1850) are common benthic bivalves in China. A number of researchers have proposed that the latter species is a junior synonym of the former species. Because of morphological similarities, it is difficult to distinguish these two species based on visual examination only. For better understanding of their taxonomy, the mitochondrial COI gene fragments of five individuals of A. divaricata from the East China Sea and six individuals of A. mirabilis from the Yellow Sea were sequenced in this study. The phylogenetic relationships of the obtained COI sequences, together with nineteen sequences of three species of the genus Nucula, were analyzed. The pairwise intra- and inter-specific distances for the COI sequences ranged from 0.002 to 0.017 and from 0.128 to 0.134, respectively, and no overlap was found. Phylogenetically, A. divaricata and A. mirabilis form distinct clades and cluster into a sister to all other Nucula species. The results indicated that A. divaricata and A. mirabilis are two distinct species. The differences in the morphology and distribution between the two species were briefly discussed.     

Community structure changes of macrobenthos in the South Yellow Sea

The ecological environment in the Yellow Sea has changed greatly from the 1950s to 1990s and this has had significant impact on marine organisms. In this study, data on soft-sediment macrobenthos occurring in depths from 25 m to 81 m in the South Yellow Sea were used to compare changes in community structure. The agglomerative classification (CLUSTER) and multidimensional scaling (MDS) methods were applied. Five communities were recognized by cluster analysis: 1. The Yellow Sea Cold Water Mass community dominated by cold water species, which changed slightly in species composition since the 1950s; 2. The mixed community with the coexistence of cold water species and warm water species, as had been reported previously; 3. The polychaete-dominated eurythermal community in which the composition changed considerably as some dominant species disappeared or decreased; 4. The Changjiang (Yangtze) River Estuarine community, with some typical estuarine species; 5. The community affected by the Yellow Sea Warm Current. The greatest change occurred in the coastal area, which indicated that the change may be caused by human activities. Macrobenthos in the central region remained almost unchanged, particularly the cold water species shielded by the Yellow Sea Cold Water Mass. The depth, temperature and median grain size of sediments were important factors affecting the distributions of macrobenthos in the South Yellow Sea.     

Sequence Comparison of Partial Cytochrome b Genes of Two Coilia species

1Introduction Japanese grenadier anchovy,Coilia ectenes Jordanet Seale(1905),is distributed in the northwest Pacif-ic.The congener,Osbeck's grenadier anchovy,Coil-ia mystus(Linnaeus,1758),is widely distributed inthe west Pacific.Both species inhabit coastal watersand estuaries and can reach up to rivers.The twospecies are important contributors to the coastal fish-eries of China(Zheng et al.,2003).Many studies on the fishery biology of the twospecies have been conducted(Zheng et al.,2003)…     

Taxonomic and genetic status of lancelet in Weihai coastal waters based on mitochondrial DNA sequence

Lancelets (subphylum Cephalochordata) are a transitional species between invertebrates and vertebrates. They are currently listed in the Second Order of Protected Animals in China. Lancelets were first documented in the waters around the city of Weihai (Shandong, China) in 2002. However, little is known about the phylogeny of this population. We analyzed the sequences of cytochrome b (Cyt b) and cytochrome oxidase c subunit I (CO I) genes from samples collected from coastal waters in the cities of Weihai and Qingdao (~150 km to the south). We analyzed 176 sequences, of which 150 were novel sequences and 26 were obtained from GenBank. Our results suggest that (1) lancelets in the two cities belong to the species Branchiostoma japonicus and have a high level of genetic diversity; (2) there is a high level of gene flow and low level of genetic differentiation between lancelets from the two cities; (3) demographic expansion occurred an estimated 1.1 million years (Ma) ago (mid Pleistocene) for lancelets in Weihai-Qingdao; and (4) the divergence between B. belcheri and B. japonicus was estimated at between 37.75 Ma (early Oligocene)-46.5 Ma (late Eocene).     

Physicochemical conditions in affecting the distribution of spring phytoplankton community

To better understand the physicochemical conditions in af fecting regional distribution of phytoplankton community, one research cruise was carried out in the Bohai Sea and Yellow Sea during 3 rd and 23 th May, 2010. The phytoplankton community, including Bacillariophyta(105 taxa), Pyrrophyta(54 taxa), Chrysophyta(1 taxon) and Chlorophyta(2 taxa), had been identified and clearly described from six ecological provinces. And, the six ecological provinces were partitioned based on the top twenty dominant species related with notable physicochemical parameters. In general, the regional distributions of phytoplankton ecological provinces were predominantly influenced by the physicochemical properties induced by the variable water masses and circulations. The predominant diatoms in most of water samples showed well adaptability in turbulent and eutrophic conditions. However, several species of dinoflagellates e.g., Protoperidinium conicum, Protoperidinium triestinum, Protoperidinium sp. and Gymnodinium lohmanni preferred warmer, saltier and nutrient-poor environment. Moreover, the dinoflagellates with high frequency in the Yellow Sea might be transported from the Yellow Sea Warm Current. The horizontal distribution of phytoplankton was depicted by diatoms and controlled by phosphate concentration, while the vertical distribution was mainly supported by light and nutrients availability in the subsurface and bottom layers, respectively.     

奥尼罗非鱼杂交子代及亲本mtDNA D-loop基因序列的多态性

利用PCR技术扩增奥利亚罗非鱼(Oreochromis aureus)、尼罗罗非鱼(O.niloticus)及其杂交子代(O.aureus♂×O.niloticus♀)3个群体mtDNA控制区全序列,分析其变异和遗传结构。结果显示:3个群体的mtDNA控制区序列长度多态性并不十分明显,全长921～933bp;3个群体间存在丰富的DNA序列多态性,共检测到138个变异位点(14.9%),44个个体具有44种单倍型(haplotype);3群体间的序列差异平均为4%,Tamura-Nei遗传距离平均为5.1%;采用NJ法和ME法构建的分子系统树中,奥利亚罗非鱼群体内所有的单倍型聚成一支,尼罗罗非鱼与其杂交子代的单倍型混杂在一起,聚成一支,表明杂交后代mtDNAD-loop表现为母系遗传。     

Complementary DNA sequencing (cDNA): an effective approach for assessing the diversity and distribution of marine benthic ciliates along hydrographic gradients

The Yellow Sea Cold Water Mass(YSCWM) is a distinct hydrographic phenomenon of the Yellow Sea,and the distribution pattern of meio-and macrobentho s diffe rs inside and outside of the YSCWM.However,such a pattern has never been observed in the microbenthic ciliate communities.Therefore,we hypothesized that benthic ciliates followed a similar distribution pattern as meio-and macrobentho s,but this pattern has not been uncovered by morphological methods.We evaluated the diversity and distribution of benthic ciliates at five stations along hydrographic gradients across the YSCWM and adj acent shallow water by using morphology and DNA and complementary DNA(cDNA) high-throughput sequencing of the V4 region of 18 S rRNA gene.Results showed that the diversity of benthic ciliate s detected by DNA(303 OTU s),and the cDNA(611 OTUs) sequencing was much higher than that detected by the morphological method(79 species).Morphological method detected roughly different ciliate communities inside and outside of the YSCWM,but without statistical significance.No clear pattern was obtained by DNA sequencing.In contrast,cDNA sequencing revealed a distinct distribution pattern of benthic ciliate communities like meioand macrobenthos,which coincided well with the results of the environmental parameter analysis.More than half of the total sequences detected by DNA sequencing belonged to planktonic ciliates,most(if not all) of which were recovered from historic DNA originating through the sedimentation of pelagic forms because none of them were observed morphologically.The irrelevant historic DNA greatly influenced the recovery of rare species and thus limited the understanding of the benthic ciliate diversity and distribution.Our research indicates that the methods used have significant effects on the investigation of benthic ciliate communities and highlights that cDNA sequencing has great advantages in estimating the diversity and distribution of benthic ciliates,as well as the potential for benthic environmental assessments.     

Foraminiferal Changes and Response to the Channel Diversion and Discharge Fluctuation of the Yellow River in the North Yellow Sea During the Past Century

Diversion of the Yellow River is a unique geological event in offshore China, causing changes of the sedimentary environment in eastern China Seas. The last diversion took place in AD 1855, with the estuary diverted from the Yellow Sea into the Bohai Sea. The identification of the river diversion events in the shelf sediments would not only provide the definite ages for the sediments, but also give a clue for better understanding of the sedimentation in that area. In this study, 210 Pb, grain size, geochemical element, and foraminiferal data in core H205 from the north Yellow Sea were systematically investigated. A high-resolution sedimentary record was established, which was coupled with the Yellow River diversion and runoff changes. The results show that the foraminiferal composition and foraminiferal abundance of the sediments from the north Yellow Sea had good response to the Yellow River diversion in 1855. Before the change, shallow water assemblages dominated the foraminifera, and the abundance of each foraminiferal species was very low. After the diversion event, the abundance of most foraminifera increased sharply, with a maximum increase of 16 times, and the assemblage was still dominated by shallow water species. Furthermore, the changes in foraminiferal abundance in the core sediments corresponded well with the discharge fluctuation of the Yellow River since 1855. When the Yellow River began entering the Bohai Sea, the Yellow River water, which is rich in nutrients, along with the coastal currents affected the north Yellow Sea, increased the primary productivity in the north Yellow Sea, which is the main reason for the abrupt increase and fluctuation of foraminiferal abundance in this area. At the meantime, the East Asian winter monsoon could also promote the development of nearshore foraminiferal species by enhancing the coastal currents.     

A preliminary phylogenetic analysis of Luidia (Paxillosida: Luidiidae) from Chinese waters with cytochrome oxidase subunit I (COI) sequences

Luidia Forbes (Paxillosida: Luidiidae) are common soft bottom sea stars with 49 described species. Because of substantial morphological diversity, the taxonomy of the genus is complex and hasn’t been resolved definitely. In order to resolve general taxonomic issues, and determine species boundaries and phylogenetic relationships within the genus Luidia, the sequences of cytochrome oxidase subunit I (COI) gene from 24 specimens of Luidia, belonging to eight taxa in Chinese waters, were studied. Three sequences of two species in genus Luidia from GenBank were used to analyze the phylogenetic relationships. The molecular phylogeny exhibited three main clades, each with strong bootstrap support: Clade A including Luidia quinaria from the Sea of Japan; Clade B including seven nominal species (L. quinaria von Martens, L. yesoensis Goto, L. changi Liu, Liao and Li, L. orientalis Fisher, L. avicularia Fisher, L. longispina Sladen and L. hardwicki Gray) from Chinese waters; and Clade C including L. maculata Müller & Troschel from Chinese waters. Our molecular phylogeny results support the morphological Quinaria-Group and Alternata-Group assigned by Döderlein. Seven nominal species we sampled do not exhibit genetic distances that are large enough to recognize them as separate species. Cryptic species may exist in’ Luidia quinaria’ from the Yellow Sea and the Sea of Japan. Meaningful morphological characters need further investigation in Luidia.     

The Clam Cyclina sinensis (Gmelin) Phylogeography Study with 28S rRNA Gene and Potential of Nuclear rRNA Genes in Genetic Assessments of Molluscs

Intraspecific diversity of molluscan species is usually studied based on maternally inherited mitochondrial DNA,from which only part of the evolutionary history can be reflected.Some nuclear ribosomal RNA genes such as 28S rRNA represent poten-tial candidates that can be easily applied in phylogeography because of lacking intraindividual variation.However,considering their low polymorphism,genetic appraisals on whether and how they can be used in population studies are necessary.Here,we applied a short 28S rRNA to assess genetic patterns of the clam Cyclina sinensis along the coast of China and compared the results with a for-mer study based on COI and ITS-1 analyses.The results revealed the 28S rRNA data set was characterized by an extremely low level of variation,with only seven haplotypes defined for 93 individuals.Haplotype and nucleotide diversity for each population was al-most the lowest when compared with the other two markers.However,the distribution of two dominant haplotypes showed clear geo-graphic patterns,and significant population differentiation was revealed between the East China Sea and the South China Sea.These patterns were highly concordant with findings of the former study that populations of C.sinensis were historically separated by land bridges among sea basins.Our study suggested that although the nuclear rRNAs have shortcomings such as low variation,they have advantages including lack of intraindividual variation and high amplification rates.Applying rRNA genes can enrich the toolbox of nuclear markers in molluscan phylogeographic studies.     

Winter Phytoplankton Assemblages of Coastal Yellow Sea Connected to Jiaozhou Bay,China

I Introduction Phytoplankton play an important role in the primary production of ocean (Ning et al., 1995). They are impor-tant biological mediators of carbon turnover in seawater ecosystems (Zhu et al., 1993). Phytoplankton in Jiaozhou Bay have been preliminarily studied on the subjects of community structure, primary productivity and carbon budget (Qian et al., 1983; Guo et al., 1992; Jiao et al., 1994). It has been found that seasonal variation of phytoplankton cell abundance presents w…