Genetic variation within and among range-wide populations of three ecotypes of the Japanese grenadier anchovy Coilia nasus with implications to its conservation and management

Studies of range-wide populations can contribute to the comprehension of the relative roles of historical events and contemporary factors that influence genetic variation within and among populations.Japanese grenadier anchovy,Coilia nasus,is a commercially important fish,which widely distributes in the Changjiang River,the coasts of China and Korea,and the Ariake Sea of Japan.This species exhibits three life-history strategies(anadromous,landlocked and freshwater resident forms).Using two fragments of nuclear DNA,genetic variation within and among 18 populations across the rivers and coast of China and Ariake Sea of Japan was examined.Patterns of genetic diversity and divergence among populations varied widely across C.nasus'range,and indicated the different effects of historical events and anthropogenic factors.Strong genetic divergence between freshwater resident populations and other populations suggested that historical geographical factors greatly influenced the genetic structure of C.nasus.Significant genetic differentiation observed among lakes in lower Changjiang River and Huaihe River might be probably influenced by hydraulic facilities.The population genetic structure among the three ecotypes revealed in the present study indicated an important role for environment variation,and the factors responsible for shaping C.nasus different life history strategies might also impact population structure.     

Changes in the population structure of Calanus sinicus during summer–autumn in the southern Yellow Sea

Calanus sinicus is a calanoid copepod widely distributed in coastal waters of China and Japan, and oversummering strategies may have major impacts on their population dynamics which in turn affect local marine food web structure. The abundance, stage composition, and sex composition of the planktonic copepod C. sinicus were studied from August to October 2002 in the southern Yellow Sea to understand how its population recovers from the over-summering state. Results showed that C. sinicus had low reproduction in August due to high temperature, except in waters near the Cheju Island with rich food and moderate bottom temperature, but the reproduction rates here decreased in September–October as food availability declined. When temperature dropped in September–October, C. sinicus actively propagated in coastal shallow waters. However, reproduction rates of C. sinicus individuals inhabiting the Yellow Sea Cold Water Mass(YSCWM) remained low during the three months of the study. The percentage of C. sinicus females was high during the reproductive period, which suggests that the sex composition of adult C. sinicus may reflect whether or not the population is in the reproductive mode.Numerous fifth copepodite stage(CV) C. sinicus aggregated in the YSCWM in a suspended developmental stage during the three months of this study, and they potentially served as the parental individuals for population development when conditions became optimal for reproduction later in the year.     

Lack of mitochondrial genetic structure in the endangered giant clam populations of Tridacna maxima (Bivalvia: Cardiidae: Tridacninae) across the Saudi Arabian coast

The present investigation focuses on population genetic structure analysis of the endangered giant clam species Tridacna maxima across part of the Red Sea,with the main aim of assessing the influence of postulated potential barriers to gene flow(i.e.,particular oceanographic features and marked environmental heterogeneity)on genetic connectivity among populations of this poorly dispersive bivalve species.For this purpose,a total of 44 specimens of T.maxima were collected from five sampling locations along the Saudi Arabian coast and examined for genetic variability at the considerably variable mitochondrial gene cytochrome c oxidase I(COI).Our results revealed lack of population subdivision and phylogeographic structure across the surveyed geographic spectrum,suggesting that neither the short pelagic larval dispersal nor the various postulated barriers to gene flow in the Red Sea can trigger the onset of marked genetic differentiation in T.maxima.Furthermore,the discerned shallow COI haplotype genealogy(exhibiting high haplotype diversity and low nucleotide diversity),associated with recent demographic and spatial expansion events,can be considered as residual effect of a recent evolutionary history of the species in the Red Sea.     

Application of the first internal transcribed spacer(ITS-1) of ribosomal DNA as a molecular marker to population analysis in farrer''s scallop Chlamys farreri

Sequence variation of the first internal transcribed spacer of ribosomal DNA （ ITS - 1 ） was examined and its application to the study of genetic variation was explored in four populations of farter＇ s scallop Chlamys farreri. ITS - 1 fragments, with a length of about 300 bp,of 78 individuals collected from Dalian, Qingdao, Yantai in China and Korea respectively were amplified via PCR, cloned and sequenced. Intra-genomic variation was examined by sequencing several clones of single individuals. Alignment and polymorphism analysis detected 44 haplotypes and 50 polymorphic sites which consist of 30 substitutions and 20 indels, indicating a high level of polymorphisms. Sequence analysis also showed a very low level of intra-individual variation. All these features validated the feasibility of application of ITS - 1 fragment to population analysis. Polymorphism analysis showed that the Korea sample has the richest genetic variation, followed by Yantai and Qingdao samples. AMOVA （analysis of molecular variance） showed that the majority （96.26%） of genetic variation was distributed within populations and 3.74% resulted from among populations, but with P 〈 0.05 （ = 0.042）, indicating that the populations in this study have significant divergence. This output was basically concordant with the result arising from RAPD data and different from that from mitochondrial 16S rDNA sequence data. Discussion on this inconsistency was made accordingly.     

Genetic and morphological divergence in the purple sea urchin Paracentrotus lividus (Echinodermata, Echinoidea) across the African Mediterranean coast

The present investigation focuses on population structure analysis of the purple sea urchin Paracentrotus lividus across the African Mediterranean coast, with the main aim of assessing the influence of the Siculo-Tunisian Strait on gene flow disruption in this highly dispersive echinoid species. For this purpose, patterns of morphological and genetic variation were assessed among its populations from the western and eastern Mediterranean coasts. A total of 302 specimens from seven Tunisian sites were collected and examined for morphometric variability at twelve morphometric traits. Concordant results, inferred from CDA (canonical discriminant analyses), pairwise NPMANOVA (non parametric multivariate analysis of variance) comparisons and MDS (multidimensional scaling) plot, unveiled significant inter-population differences in the measured traits among the studied populations. Furthermore, the combined use of the one way ANOSIM (analysis of similarities) and the Discriminant/Hotelling analysis allowed unravelling two morphologically differentiated groups assigned to both western and eastern Mediterranean basins. The SIMPER (similarity percentages) routine analysis showed that total dry weight, test diameter and spine length were major contributors to the morphometric separation between locations and between groups. Pattern of phenotypic divergence discerned in P. lividus across the Siculo-Tunisian Strait is interestingly in congruence with that inferred from the genetic investigation of the purple sea urchin populations from the same region based on the analysis of the mtDNA COI (cytochrome oxidase I) gene in 314 specimens from nineteen locations covering a wider geographic transect, streching westward to the Algerian coast and eastward to the Libyan littoral. The specific haplotypic composition characterizing each Mediterranean basin, as inferred from the minimum spanning network, confirmed the geographic partioning of genetic variation, as revealed by F-statistics and AMOVA (analysis of molecular variance) analyses, yielding significant genetic differentiation between eastern and western Mediterranean populations. The newly detected phylogeographic patterns, observed for the first time in P. lividus throughout the explored distribution range, suggest the involvement of different biotic and abiotic processes in shaping such variation, and provide evidence that a large and geographically exhaustive dataset is necessary to unveil phylogeographic structure within widespread marine species, previously cathegorized as panmictic in part of their distribution range.     

Application of an optical nitrate profiler to high- and low-turbidity coastal shelf waters

Here, we report the results of high-resolution nitrate measurements using an optical nitrate profiler(in situ ultraviolet spectrophotometer, ISUS) along transect across a high-turbidity shelf(East China Sea) and a lowturbidity shelf(Chukchi Sea). The ISUS-measured nitrate concentrations closely reproduced the results measured by conventional bottle methods in low-turbidity waters. However, for high-turbidity waters of the East China Sea(salinity<30), a correction factor of 1.19 was required t...     

东黄海星康吉鳗渔业生物学特性研究

Whitespotted conger Conger myriaster is a commercially important species in the seas around China, Korea and Japan. The coastal waters of China serve as an important feeding ground for congers, but the spatio-temporal variations in the fishery and biological characteristics of the population have been rarely evaluated and less well understood in this area. We studied the growth, spawning and feeding characteristics of C. myriaster on the basis of samples collected from October 2016 to April 2017 in the Yellow Sea and East China Sea. A total of 529 specimens were collected, with ages ranging from 1 to 6 years and total length ranging from 132 mm to 834 mm.The parameters of von Bertalanffy growth equation L_∞ and k were 1 026 mm and 0.226 a~(–1), respectively; the sex ratio was 88:0(female: male) in the East China Sea and 2.67:1 in the South Yellow Sea; the development stage of ovary ranged from peri-nucleolus stage to secondary yolk globule stage, and the testis of two males was at midmeiotic stage; Crustacean was the major prey for conger of small length, and food source shift to fish with somatic growth. The results showed substantial differences from previous studies in Japan and Korean waters, as well as from China seas in the 1980 s, suggesting potential spatiotemporal changes in the biological characteristics of C.myriaster. This study may improve current understanding of the fishery biology of C. myriaster in the Yellow Sea and East China Sea.     

Spatial and temporal variations of macro-and mesozooplankton community in the Huanghai Sea (Yellow Sea) and East China Sea in summer and winter

The study was conducted during two cruises of June–August 2006 (summer),and January–February 2007 (winter) in the Huanghai (Yellow) Sea and East China Sea.Spatial and temporal variations of zooplankton abundance,biomass and community structure and its relation to currents and water masses over the continental shelf were examined.A total of 584 zooplankton species/taxa and 28 planktonic larvae were identified during the two surveys.Copepods were the most abundant component among these identified groups.Zooplankton abundance and biomass fluctuated widely and showed distinct heterogeneity in the shelf waters.Five zooplankton assemblages were identified with hierarchical cluster analysis during this study,and they were Huanghai Sea Assemblage,Changjiang Estuary Assemblage,Coastal Assemblage,East China Sea Mixed-water Assemblage and East China Sea Offshore Assemblage.Seasonal changes of zooplankton community composition and its geographical distribution were detected,and the locations of the faunistic areas overlap quite well with water masses and current systems.So we suggest that the zooplankton community structure and its changes were determined by the water masses in the Huanghai Sea and East China Sea.The results of this research can provide fundamental information for the long-term monitoring of zooplankton ecology in the shelf of Huanghai Sea and East China Sea.     

An analysis on the formation mechanism of the distribution of high content of chlorophyll-a in the continental shelf edge waters of East China Sea

On the basis of the data obtained from the comprehensive Kuroshio surveys in 1987-1988,this paper analyses the oceanographic characteristics in the area (125°-130° E,27°-31° N) of the continental shelf edge of the East China Sea (E. C. S. ) and its adjacent waters and discusses the effects of the Kuroshio front,thermocline and upwelling of the Kuroshio subsurface water on the distribution of standing stock of phytoplankton (chlorophyll-a). The distribution of high content of chlorophylly-a has been detected at 20-50 in depth in the water body on the left side of the Kuroshio front in the continental shelf edge waters of the E. C. S. The high content of chlorophyll-a spreads from the shelf area to the Kuroshio area in the form of a tongue and connects with the maximum layer of subsurface chlorophyll-a of the Kuroshio and pelagic sea. The author considers that the formation of the distribution of high content chlorophyll-a in this area results from the bottom topography and oceanic environment and the     

Molecular phylogenetics and population demographic history of Amphioctopus fangsiao,inferred from mitochondrial and microsatellite DNA markers

Amphioctopus fangsiao(Cephalopoda: Octopodidae) is an important commercial species in the coastal waters of China. In recent years, however, the resource of A. fangsiao have declined because of habitat destruction and overfishing. To analyze the genetic variations of A. fangsiao caused by the fluctuation of resources, the population genetic structure of nine sampling locations collected from the Bohai Sea to the South China Sea were investigated, using mtDNA COI fragments and microsatellite DNA....     

东海近岸带鱼(Trichiurus japonicus)线粒体控制区序列的群体遗传变异研究

带鱼(Trichiurusjaponicus)是广泛分布于东亚大陆架海域的暖温性近底层经济鱼类,也是东海区最重要的海洋渔业捕捞对象。然而,目前的研究报道对东海近岸带鱼群体遗传变异特性认识不足,不利于其种群的遗传资源保护和管理。本研究利用线粒体控制区序列对东海近岸带鱼6个群体191个个体的遗传多样性、遗传分化和历史动态进行分析。在577 bp长的控制区序列中共检测到70个多态位点,定义了121个单倍型。群体总的单倍型多样性较高(0.9911),但总的核苷酸多样性较低(0.0092),群体间遗传多样性水平差异较小。单倍型遗传学关系、Fst值和分子方差分析结果均表明群体间的遗传分化不显著,存在广泛的基因交流。历史动态分析结果表明东海近岸带鱼群体在更新世中晚期可能经历了瓶颈效应和随后的群体快速扩张,这是导致群体遗传多样性较低的主要原因。带鱼较强的扩散能力、洄游行为、海洋环流以及近期的群体扩张可能是造成东海近岸带鱼缺乏显著的系统地理种群结构的原因。研究结果提示,在线粒体DNA水平上,东海近岸带鱼群体是一个随机交配的种群,在遗传资源管理上可作为一个单元进行管理。     

Population Genetic Structure of Rock Bream (<Emphasis Type="Italic">Oplegnathus fasciatus</Emphasis> Temminck &amp; Schlegel, 1884) Revealed by mtDNA COI Sequence in Korea and China

The rock bream, Oplegnathus fasciatus, is a common rocky reef game fish in East Asia and recently has become an aquaculture species. Despite its commercial importance, the population genetic structure of this fish species remains poorly understood. In this study, 163 specimens were collected from 6 localities along the coastal waters of Korea and China and their genetic variation was analyzed with mtDNA COI sequences. A total of 34 polymorphic sites were detected which determined 30 haplotypes. The genetic pattern reveals a low level of nucleotide diversity (0.04 ± 0.003) but a high level of haplotype diversity (0.83 ± 0.02). The 30 haplotypes are divided into two major genealogical clades: one that consists of only Zhoushan (ZS, East China Sea) specific haplotypes from the southern East China Sea and the other that consists of the remaining haplotypes from the northern East China Sea, Yellow Sea, Korea Strait, and East Sea/Sea of Japan. The two clades are separated by approximately 330~435 kyBP. Analyses of AMOVA and F_st show a significant population differentiation between the ZS sample and the other ones, corroborating separation of the two genealogical clades. Larval dispersal and the fresh Yangtze River plume are invoked as the main determining factors for this population genetic structure of O. fasciatus. Neutrality tests and mismatch distribution analyses indicate late Pleistocene population expansion along the coastal waters of Korea and China approximately 133–183 kyBP during which there were periodic cycles of glaciations and deglaciations. Such population information needs to be taken into account when stock enhancement and conservation measures are implemented for this fisheries species.     

我国东南沿海厚壳贻贝(Mytilus coruscus)4 个群体线粒体16S rRNA 序列及遗传结构分析

采用16S rRNA基因测序技术,对我国东南沿海4个地理群体的厚壳贻贝遗传结构及遗传变异进行研究。通过对4个厚壳贻贝群体共83个个体的线粒体16S rRNA基因进行测序,获得1个长度为305bp的同源序列,共检测到150个多态位点,多态位点比例达49.18%。83个个体中共检测到28个单倍型,单倍型多样性指数(Hd)为0.810,核苷酸多样性指数(Pi)为0.09602,平均核苷酸差异数(K)达27.846。结果表明,我国东南沿海厚壳贻贝群体具有较高的遗传多样性水平。遗传结构检测结果表明,舟山群体、温州群体、宁德群体间的遗传距离小,遗传分化系数(Fst)为-0.0141—0.0059之间,群体内部无显著分化(P>0.05),而福州群体与其它群体间遗传距离较大,为0.215—0.217之间,遗传分化系数(Fst)也较大,为0.6217—0.6319之间,存在极显著的遗传分化(P<0.001)。     

我国南部海域条纹斑竹鲨线粒体DNA控制区遗传多态性研究

摘要:在对我国南部沿海闽东、闽南、粤西、海南、北部湾5个海域的条纹斑竹鲨群体线粒体控制区多态性研究中,获得长度为1 094~1 096 bp的线粒体控制区完整序列。序列比对发现了6个多态性核苷酸位点,定义了8个单倍型。5个群体的单倍型多样度(h=0.542 5~0.744 8)和核苷酸多样度(π=0.000 571~0.000 980)均处于较低水平,说明条纹斑竹鲨的线粒体DNA进化速率较低。分子方差分析(AMOVA)结果显示群体间的遗传差异较小(Fst=0.216 26,P<0.000 1),变异主要发生在群体内部。10 000步Markov链计算的群体间遗传分化概率及单倍型系统地理学分析结果将5个群体分成两个地理种群(台湾海峡种群、南海北部种群)。综合分析表明条纹斑竹鲨的基因流主要在浅海近岸水域扩散,遗传变异程度受地理结构和距离隔离影响。     

中国沿海不同地区泥蚶(Tegillarca granosa)的遗传多样性分析

以采自海南海口、广西防城港、广西北海、广东湛江、福建漳州、山东荣成、山东威海7个地理群体62个泥蚶个体为材料,获取592bp线粒体COI基因片段序列,并进行遗传多样性及分化分析。多态性遗传参数统计显示:62个个体共检测出103个多态性位点,定义了26个单倍型;总群体单倍型多样性指数为0.834,核苷酸多样性指数为0.01665,平均核苷酸差异数为9.85772。7个群体均显示出较丰富的遗传多样性,群体内遗传距离及群体内遗传多样性参数显示中国沿海泥蚶遗传多样性由北向南呈升高趋势,而群体内遗传分化系数也呈现升高的趋势。基于26个单倍型COI序列构建的NJ树和UPGMA树以及基于群体间遗传距离构建的UPGMA树显示,荣成群体和威海群体亲缘关系较近,聚成一小支,而后与漳州群体相聚,然而南方类群并没有聚为独立的一支。     

根据mtDNA D-loop 序列分析东海银鲳群体遗传多样性

根据线粒体D-loop序列对舟山群岛附近海域的银鲳(Pampus argenteus)群体(n=24)的遗传多样性进行了研究。通过PCR技术对线粒体D-loop序列进行扩增,获得大小约为500bp的扩增产物。PCR产物经纯化并进行序列测定后,得到了357bp的核苷酸片段。在24个个体中,共检测到14个变异位点,其中8个转换位点,5个颠换位点,1个转换与颠换同时存在的位点。运用MEGA软件计算出不同个体间的遗传距离,并根据其遗传距离构建了UPGMA和NJ系统树。DNASP软件计算出的单倍型多样性(h)、核苷酸多样性(π)及平均核苷酸差异数(k)分别为0.89、0.007与2.57。此外,岐点分布及中性检验显示,东海银鲳群体在历史上可能经历过种群扩张。研究结果表明,线粒体D-loop基因可用于银鲳群体内及群体间遗传多样性的分析。     

南沙群岛密斑马面鲀群体遗传多样性分析

密斑马面鲀Thamnaconustessellatus是在我国南海海域较为常见的一种马面鲀属鱼类。本研究基于线粒体DNA控制区序列对南沙群岛密斑马面鲀3个群体的遗传结构及其遗传多样性进行了分析。研究结果显示,密斑马面鲀的控制区序列变异程度较大,86尾个体序列的变异位点数为38个,共定义了28个单倍型;3个密斑马面鲀群体的单倍型多样度和核苷酸多样度均较高,且相差不大;密斑马面鲀群体间未检测到显著的群体遗传结构,分子方差分析表明,99.67%的遗传差异来自于群体内,群体间遗传差异仅为0.33%。贝叶斯树和最大似然树均显示出密斑马面鲀单倍型间松散的分布,未检测到显著的谱系结构。群体历史动态分析结果表明密斑马面鲀的群体经历了更新世的群体扩张事件。     

基于线粒体控制区的中国近海竹荚鱼种群遗传结构和种群历史动态分析

竹荚鱼(Trachurus japonicus)是中国近海主捕鱼种之一, 在海洋食物网中扮演了重要角色, 然而环境污染和过度捕捞导致其出现种群数量衰退以及个体趋于小型化等现象。为了解中国近海竹荚鱼的种群遗传格局, 文章以线粒体DNA控制区为遗传标记研究了东海大陆架、福建近海和南海北部湾竹荚鱼群体的遗传结构以及种群历史动态。结果表明, 中国近海竹荚鱼整体呈现高单倍型多态性(H_d=0.998±0.001)和高核苷酸多态性(π=0.01259±0.00041)的遗传多样性特征。单倍型网络图呈现为星形辐射状的单一谱系, 利用最大似然法构建的系统进化树也未发现谱系分化。不同海区地理群体的分子方差分析显示东海群体和南海北部湾群体间无遗传分化, 遗传变异主要来源于群体内部(99.39%)。中性检验和核苷酸歧点分布分析结果暗示各海区竹荚鱼群体(东海、南海北部湾)以及整个群体均经历过近期的种群扩张。中国近海竹荚鱼群体呈现为遗传均匀的种群结构, 可以作为一个单一的种群加以管理, 人类高强度捕捞压力尚未影响其种群恢复潜力。     

中国近海外来囊藻(Colpomenia peregrina)种群遗传多样性研究

外来囊藻(Colpomeniaperegrina)是一种在潮间带分布广泛的褐藻,它能附着在牡蛎壳上进行跨海区扩散,因而是研究生物多样性变动和生物地理格局形成的良好模型。外来囊藻在中国沿海虽有分布,但关于其种群遗传多样性和分化研究的报道尚为空白。本研究采集了中国近海13个外来囊藻种群样本。通过扩增301条线粒体cox3序列,发现了26个单倍型;通过重建单倍型网络图和基于最大似然法与贝叶斯法重建系统进化树,发现外来囊藻种内遗传多样性较高, 13个种群划分为3个遗传世系,其中浙江南麂列岛的7个种群组成遗传世系A,辽宁和山东的样本则分化为遗传世系B和C。中国近海外来囊藻的这种种群遗传结构可能源于更新世末次盛冰期黄渤海、东海边缘海的环境变化和海平面的大幅下降。遗传世系A具有的较高单倍型多样性,其原因可能是南麂列岛独特的地理位置和潮间带环境的共同作用。     

A pilot study of genetic differentiation between two phenotypes of a Mediterranean population of the bivalve Cerastoderma glaucum and genetic discrimination with other Cerastoderma glaucum and Cerastoderma edule populations outside the Mediterranean

The internal transcribed spacer 1 (ITS1) region of 29 individuals of Cerastoderma glaucum (from the Mediterranean Sea, the Atlantic and the North Sea) and 18 individuals of Cerastoderma edule (from the Atlantic and the North Sea) and the cytochrome c oxidase subunit I (COI) region of 43 individuals of C. glaucum (from the Mediterranean Sea, the Atlantic and the North Sea) and 9 individuals of C. edule (from the Atlantic and the North Sea) were PCR amplified and sequenced. The ITS1 sequences led us to describe 27 genetic haplotypes, while 21 genetic haplotypes were determined via the COI sequences. The ITS1 and the COI sequences revealed an important genetic variability within the Mediterranean population of C. glaucum, which contained two different phenotypes: orange foot and yellow foot. A genetic differentiation between the two phenotypes was revealed by the nucleotide diversity index (π) and is strengthened by the AMOVA analysis. This result leads us to suspect the presence of two different groups in the same population of C. glaucum. Nevertheless to be confirmed this hypothesis requires further studies using more locations and a larger number of sample sizes.