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（Cyt b）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531～544 bp（16S）、652～675 bp（COⅠ）和406～453 bp（Cyt b）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%,Cyt b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;Cyt b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、03156、0.2361）.认为3种星虫线粒体16S rRNA、COⅠ和Cyt b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.     

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。     

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。     

4种鲷科鱼种内细胞色素b基因序列的保守性

对真鲷 (Pagrosomusmajor)、黄鳍鲷 (Sparuslatus)、黑鲷 (S .macrocephalus)和平鲷 (Rhabdosar gussarba )的线粒体DNA细胞色素b 4 0 5bp序列进行测定。结果发现 ,4种鲷科鱼种内碱基的变异较低 ,真鲷为 0 .2 5% ,黄鳍鲷为 0 .74 % ,黑鲷和平鲷均为 0 ;真鲷有 4种单倍型 ,黄鳍鲷有 2种单倍型 ,黑鲷和平鲷分别为 1种单倍型 ,且单倍型间变异位点很少 ,真鲷有 3个变异位点 ,黄鳍鲷仅有 1个变异位点 ,而黑鲷和平鲷无变异位点。结果表明 ,细胞色素b基因在这 4种鲷科鱼种内是相当保守的。     

4种鲷科鱼种内细胞色素b基因序列的保守性

对真鲷(Pagrosomus major)、黄鳍鲷(Sparus latus)、黑鲷(S.macrocephalus)和平鲷(Rhabdosargus sarba)的线粒体DNA细胞色素b 405bP序列进行测定。结果发现，4种鲷科鱼种内碱基的变异较低，真鲷为0．25％，黄鳍鲷为0．74％，黑鲷和平鲷均为0；真鲷有4种单倍型，黄鳍鲷有2种单倍型，黑鲷和平鲷分别为1种单倍型，且单倍型间变异位点很少，真鲷有3个变异位点，黄鳍鲷仅有1个变异位点，而黑鲷和平鲷无变异位点。结果表明，细胞色素b基因在这4种鲷科鱼种内是相当保守的。     

基于cox1条形码的鱼肚DNA分子鉴定

为鉴定鱼肚的正品来源,运用一对特异性引物扩增并测定10 个不同价格（700～1 500 元/kg）鱼肚样本的线粒体DNA 细胞色素c 氧化酶Ⅰ（cox1）约660 bp 的序列.通过BLASTN 比对DNA 序列同源度,判定鱼肚所属种类分别为鲈形目石首鱼科（Sciaenidae）、马鲅科（Eleutheronema）、笛鲷科（Lutjanidae）、带鱼科（Trichiuridae）.cox1 条码序列获取便捷,基于此条码序列的物种鉴定技术可用于鱼肚种类鉴别.     

卵形鲳鲹肉碱棕榈酰基转移酶Ⅰ全长cDNA序列的克隆及生物信息学分析

采用RACE-PCR克隆卵形鲳鲹(Trachinotus ovatus)肉碱棕榈酰基转移酶Ⅰ(carnitine palmitoyltransferaseⅠ,CPTⅠ)c DNA序列全长,并对其编码氨基酸进行生物信息学分析。结果表明,卵形鲳鲹CPTⅠ基因(Gen Bank登录号KP987456)c DNA序列全长2 841 bp,其开放阅读框(ORF)为2 363 bp,编码787个氨基酸,3'非编码区(URT)335 bp,5'非编码区142 bp;生物信息预测显示CPTⅠ基因编码的蛋白无信号肽序列,脂溶指数高达85.63,亲水性平均值(GRAVY)为-0.213,具有2个跨膜区螺旋,在第312和367氨基酸残基处存在N-糖基化位点,在19个丝氨酸(Ser)、9个苏氨酸(Thr)和14个酪氨酸(Tyr)残基上可能发生磷酸化;二级结构中α螺旋(Alpha helix)占比例最大,为40.66%;该蛋白亚细胞定位预测其主要分布于细胞质和线粒体中;分子系统进化分析显示,卵形鲳鲹CPTⅠ蛋白与花鲈(Lateolabrax japonicas)的同源性最高,达94%,与大黄鱼(Larimichthys crocea)、金鲷(Sparus aurata)的次之,均为93%,与人(Homo sapiens)、鼠(Mus musculus)等的同源性较低(65%)。     

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)。     

近50 a ENSO时频特征及其与南海台风的相关性

【目的】分析表征ENSO事件的特征值和南海台风活动的多时间尺度结构特征及其相关关系。【方法】采用日本气象厅东京台风中心(JMA)1967-2016年西北太平洋TC最佳路径数据集,统计分析了近50 a来南海台风活动月频数。同时又采用Morlet小波变换、交叉小波变换、小波相干等方法,分析了近50 a来ENSO事件时频变化特征及其与南海台风相关性。【结果与结论】ENSO循环具有2-6 a的主周期;7-10月南海台风活动最为频繁,其频数时间序列存在准2 a尺度周期;ENSO指数与南海台风活动频数的相关表现在多个时间尺度上。1970-1978年、1995-2000年,ONI指数和南海台风活动频数在2-6 a周期尺度上具有较好的相关关系,并且南海台风活动频数变化先于ONI指数半个周期。1980-1985年间,在1.5-3 a的周期尺度上SOI指数和南海台风活动频数具有较好的相关关系,且两序列同步变化。     

辽宁海城小孤山披毛犀化石的古DNA分析

从采自辽宁省海城县小孤山晚更新世披毛犀化石样品中成功地获得了1080bp细胞色素b 基因序列,调用Genbank中
已发表的披毛犀序列及5种现生犀牛的同源序列,以马作为外类群,采用邻接法(NJ法)和最大似然法(ME法)构建系统发育树,
结果均显示披毛犀与现生苏门答腊犀亲缘关系最近,且辽宁省海城县小孤山样品处于披毛犀分支的根部;对披毛犀样品进行基因
分异度分析结果表明,小孤山的披毛犀样品具有较高的基因分异度,为探讨披毛犀的起源、迁徙及演化等问题提供了重要的分子
依据。      

The Complete Sequence of Mitochondrial COⅡ Gene of Fenneropenaeus chinensis and Its Applicability as a Marker for Phylogenetic Analysis

The complete mitochondrial cytochrome oxidase subunit Ⅱ (COⅡ) gene of Penaeinae shrimp Fenneropenaeus chinensis was cloned and sequenced. The gene is 688 bp in length and codes for 229 amino acids. It shows 83.2%, 87.0% and 83.8% sequence similarity to Marsupenaeus Japonicus, Penaeus monodon and Farfantepenaeus notialis, respectively. The A+T content of the whole gene and that at the third position of codons are 64.7% and 78.2%, respectively. The phylogenetic relationship between F. chinensis and three other species representing genera Farfanatepenaeus, Marsupenaeus and Penaeus was analyzed. Results showed that the genetic distances among the four taxa ranged from 0.144 0 to 0.200 5, exceeding those estimated with COⅠ and partial 16S rRNA gene sequences among Marsupenaeus, Litopenaeus and Melicertus, and being therefore larger than the value among subgenera. It has been suggested that the COⅡ gene has a faster evolutionary rate than that of the COⅠ gene and partial 16S rRNA gene and could be used for phylogenetic analysis at genus or species level. The results of the present study indicated that Farfantepenaeus, Fenneropenaeus, Marsupenaeus and Penaeus are at a higher phylogenetic level than subgenus, which supports the opinion of the elevation of phylogenetic status of the four subgenera to genus level.     

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。     

Monsoon-ocean coupled modes in the South China Sea and their linkage with the eastern Indian Ocean-western Pacific warm pool

Monsoon-ocean coupled modes in the South China Sea （SCS） were investigated by a combined singular value decomposition （CSVD） analysis based on sea surface temperature （SST） and sea surface wind stress （SWS） fields from SODA （Simple Ocean Data Assimilation） data spanning the period of 1950-1999. The coupled fields achieved the maximum correlation when the SST lagged SWS by one month, indicating that the SCS coupled system mainly reflected the response of the SST to monsoon forcing. Three significant coupled modes were found in the SCS, accounting for more than 80% of the cumulative squared covariance fraction. The first three SST spatial patterns from CSVD were： （Ⅰ） the monopole pattern along the isobaths in the SCS central basin; （Ⅱ） the north-south dipole pattern; and （Ⅲ） the west-east seesaw pattern. The expansion coefficient of the SST leading mode showed interdecadal and interannual variability and correlation with the Indo-Pacific warm pool （IPWP）, suggesting that the SCS belongs to part of the IPWP at interannual and interdecadal time scales. The second mode had a lower correlation coefficient with the warm pool index because its main period was at intra-annual time scales instead of the interannual and interdecadal scales with the warm pools. The third mode had similar periods to those of the leading mode, but lagged the eastern Indian Ocean warm pool （EIWP） and western Pacific warm pool （WPWP） by five months and one year respectively, implying that the SCS response to the warm pool variation occurred from the western Pacific to the eastern Indian Ocean, which might have been related to the variation of Indonesian throughflow. All three modes in the SCS had more significant correlations with the EIWP, which means the SCS SST varied much more coherently with the EIWP than the WPWP, suggesting that the SCS belongs mostly to part of the EIWP. The expansion coefficients of the SCS SST modes all had negative correlations with the Nino3 index, which they lag by several months, indicating a remote response of SCS SST variability to the El Nifio events.     

Water masses in the South China Sea and water exchange between the Pacific and the South China Sea

Water masses in the South China Sea (SCS) were identified and analyzed with the data collected in the summer and winter of 1998. The distributions of temperature and salinity near the Bashi Channel (the Luzon Strait) were analyzed by using the data obtained in July and December of 1997. Based on the results from the data collected in the winter of 1998, waters in the open sea areas of the SCS were divided into six water masses: the Surface Water Mass of the SCS (S), the Subsurface Water Mass of the SCS (U), the Subsurface-Intermediate Water Mass of the SCS (UI), the Intermediate Water Mass of the SCS (I), the Deep Water Mass of the SCS (D) and the Bottom Water Mass of the SCS(B). For the summer of 1998, the Kuroshio Surface Water Mass (KS) and the Kuroshio Subsurface Water Mass (KU) were also identified in the SCS. But no Kuroshio water was found to pass the 119.5°E meridian and enter the SCS in the time of winter observations. The Sulu Sea Water (SSW) intruded into the SCS through the Mindoro Channel between 50–75 m in the summer of 1998. However, the data obtained in the summer and winter of 1997 indicated that water from the Pacific had entered the SCS through the northern part of the Luzon Strait in these seasons, but water from the SCS had entered the Pacific through the southern part of the Strait. These phenomena might correlate with the 1998 El-Niño event.     

Sea surface temperature anomalies in the South China Sea during mature phase of ENSO

Based on the 18-year(1993–2010) National Centers for Environmental Prediction optimum interpolation sea surface temperature(SST) and simple ocean data assimilation datasets,this study investigated the patterns of the SST anomalies(SSTAs) that occurred in the South China Sea(SCS) during the mature phase of the El Ni?o/Southern Oscillation.The most dominant characteristic was that of the outof-phase variation between southwestern and northeastern parts of the SCS,which was influenced primarily by the net surface heat flux and by horizontal thermal advection.The negative SSTA in the northeastern SCS was caused mainly by the loss of heat to the atmosphere and because of the cold-water advection from the western Pacific through the Luzon Strait during El Ni?o episodes.Conversely,it was found that the anomalous large-scale atmospheric circulation and weakened western boundary current during El Ni?o episodes led to the development of the positive SSTA in the southwestern SCS.     

Anomalies of asian summer monsoon related to ssta in the south China Sea and the tropical pacific

ＩＮＴＲＯＤＵＣＴＩＯＮＴｈｅＳｏｕｔｈＣｈｉｎａＳｅａ(ＳＣＳ)ｉｓａｐａｒｔｌｙ ｅｎｃｌｏｓｅｄｏｃｅａｎｂａｓｉｎｏｖｅｒｌａｉｄｂｙａｐｒｏｎｏｕｎｃｅｄｍｏｎｓｏｏｎｓｕｒｆａｃｅｗｉｎｄ .Ｐａｓｔｓｔｕｄｉｅｓ (Ｃｈｅｎｅｔａｌ.,1 991 ;ＤｉｎｇａｎｄＭｕｒａｋａｍｉ,1 994 ;Ｙａｎ ,1 997;ＬｉａｎｇＢｉｑｉ,1 991 ;ＬｉａｎｇＪｉａｎｙｉｎ ,1 991 )ｉｎｄｉｃａｔｅｔｈａｔａｈｕｇｅｗａｒｍｗａｔｅｒｐｏｏｌｊｏｉｎｔｌｙｃｏｎｔｒｉｂｕｔｅｄｂｙｔｈｅｗｅｓｔｅｒｎＰａｃｉｆｉｃ ,ｅａ…     

Modulation of tropical cyclogenesis over the South China Sea by ENSO Modoki during boreal summer

This study examines the modulation of tropical cyclogenesis over the South China Sea(SCS) by the El Nio-Southern Oscillation(ENSO) Modoki during the boreal summer. Results reveal that there were more tropical cyclones(TCs) formed over the SCS during central Pacific warming years and less TC frequency during central Pacific cooling years. How different environmental factors(including low-level relative vorticity, mid-level relative humidity, vertical wind shear, and potential intensity) contribute to this influence is investigated, using a genesis potential(GP) index developed by Emanuel and Nolan. Composite anomalies of the GP index are produced for central Pacific warming and cooling years separately, which could account for the changes of TC frequency over the SCS in different ENSO Modoki phases. The degree of contribution by each factor is determined quantitatively by producing composites of modified indices in which only one of the contributing factors varies, with the others set to climatology. The results suggest that the vertical wind shear and low-level relative vorticity, which are associated with the ENSO Modoki-induced anomalous circulations in Matsuno-Gill patterns, make the largest contributions to the ENSO Modoki modulation of tropical cyclogenesis over the SCS as implied by the GP index. These results highlight the important roles of dynamic factors in the modulation of TC frequency over the SCS by the ENSO Modoki during the boreal summer.