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.     

历史DNA在鱼类群体遗传与进化研究中的应用

历史耳石、鳞片作为鱼类群体遗传与进化研究宝贵的DNA来源,记录了几十年甚至几百年间的遗传信息,使得鱼类群体遗传与进化研究可以扩展到历史时间尺度,从而可以直接反映人类活动对鱼类遗传多样性及适应性进化的影响。近十几年来,随着高通量测序技术的蓬勃发展,历史耳石、鳞片作为基因组数据的来源成为现实,可提供更为精细的遗传数据。然而,历史样本具有DNA高度降解、外源DNA污染等特点,利用历史DNA进行群体遗传学研究仍然是一项十分困难的工作。作者对历史耳石、鳞片样本DNA的提取方法,基因分型技术进行了总结,以期为克服这些困难提供思路。另外,作者综述了利用历史样本进行鱼类群体遗传与进化研究的现状与热点。伴随新一代分子技术的普及与发展,历史DNA可以提供更为丰富的遗传信息,将为鱼类群体遗传与进化相关研究提供新的思路与证据,未来势必拥有更广阔的应用前景。     

基于DNA条形码研究中国枪乌贼和鸢乌贼的食物种类组成*

中国枪乌贼(Uroteuthis chinensis)和鸢乌贼(Sthenoteuthis oualaniensis)作为中国南海头足类的关键种, 对海洋生态系统的物质流动与能量循环具有重要影响, 其摄食生态的研究将对海洋食物网的构建具有重要意义。由于传统胃含物分析法难以准确鉴定糜状饵料生物的组成, 本研究利用DNA条码技术, 针对中国枪乌贼和鸢乌贼不可辨认的食物糜提取组织DNA, 选用线粒体基因细胞色素C氧化酶亚基I(Mitochondrial cytochrome oxidase subunit I, COI)作为分子标记, 获得的序列在Genbank中进行比对分析, 并使用GMYC(Generalized Mixed Yule Coalescent)模型进行物种界定和构建系统进化关系。结果成功鉴定出中国枪乌贼饵料物种有13种, 鸢乌贼饵料物种有8种, 共20种(其中1种为共有饵料)。比较发现, 汕头-台湾浅滩渔场的中国枪乌贼主要摄食鱼类、甲壳类和头足类, 而南海中部海域鸢乌贼则主要摄食鱼类和头足类。两物种均存在同类相食现象, 但鸢乌贼表现更明显。     

Evaluation of DNA Damage in the Marine Mussel Crenomytilus grayanus as a Genotoxic Biomarker of Pollution

Marine pollution affects all life processes in aquatic organisms. The genotoxic effect of pollution on the mussel Crenomytilus grayanus was assessed. Bivalves were collected from the ‘clean'(Vostochnaya Cove) and polluted(Nakhodka Bay) areas in the Peter the Great Bay. The degree of DNA damage in C. grayanus was determined by alkaline comet assay as mean percentage of DNA in tail, and the genetic damage index was calculated. Our results indicate that almost one-third of DNA in cells of gills and digestive gland of C. grayanus inhabiting the Nakhodka Bay had destructive changes compared to the individuals of this species from the Vostochnaya Cove. This study has shown that chronic pollution of the aquatic environment causes destructive changes to DNA in gill and digestive gland cells of C. grayanus.     

Impaired Functions in Nile Tilapia,Oreochromis niloticus (Linnaeus, 1757), from Polluted Waters

Oreochromis niloticus is an endemic species in the River Nile and represents the main object of fishery in the Nile Delta Lakes of which Lake Maryût is the smallest and most polluted. Due to current pollution problems, fish production in the lake greatly declined. Besides fish biology, this study considered a wide array of water databases in selected sites along the lake. Hydrologic and biologic data were compared to that of a reference fish hatchery. Water concentrations of ammonia, manganese, nickel, cadmium, lead and mercury proved hazardous to fish, whereas chromium, copper, iron, zinc, pH, alkalinity, hardness, phosphate, nitrate, and nitrite always fell within acceptable levels. Physiologic evaluation of O. niloticus pointed out improper growth, protein inadequacy, and functional impairment in fish inhabiting polluted sites, in particular the lake main basin. These were reflected by data of specific formulae as RNA/DNA and the relative RNA content (r) in cells of the liver and gill arches as well as by the relative mobilization of serum protein fractions. It seems, however, that growth competence is additionally affected by the stress impact exerted upon fish by massive population numbers in some cramped commercial ponds.     

河南安阳殷墟孝民屯遗址出土家养黄牛的DNA研究

作为晚商的都城和当时最大都市的殷墟(1300~1046 BCE),家养黄牛是最重要的大型家养动物之一.殷墟的家养黄牛可以肉食、可以役用,骨料可做骨器,是最主要的祭牲,其肩胛骨还可以用于占卜、可以记载甲骨文.本文对安阳殷墟孝民屯遗址普通灰坑和祭祀坑出土的15例牛骨线粒体DNA控制区285 bp的片段进行分析研究,其中有13例获取了所需的DNA序列.DNA分析表明12例属于家养普通牛(Bos taurus),1例属于野生原始牛(Bos primigenius).殷墟孝民屯家养普通牛的单倍型类群分布频率为以T3为主约占58.3%,T4次之约占33.3%,T2最少约占8.3%,该遗传多样性在当时已经达到或保持在可能的最高水平了.推测作为都城和大都市的殷墟聚集了中国早期各个地区的黄牛.孝民屯祭祀坑和普通灰坑出土牛骨线粒体DNA单倍型类群没有明显的差异,表明孝民屯用于祭祀的黄牛没有经过特殊的"母系"筛选,但不排除有对核DNA控制的特殊体质、生理或行为等性状进行有意识地筛选,以示祭祀的神圣性和特殊性.本文有限的DNA数据显示普通灰坑出土牛骨的DNA保存相对较差,暗示着普通灰坑的牛骨作为食余废弃物可能经历了更多炊煮活动中的高温处理,坑内埋藏环境不同也可能使普通灰坑的牛骨保存状况不如祭祀坑内的牛骨,普通灰坑牛骨样本DNA降解和破坏得更厉害.     

无机砷As(Ⅲ、Ⅴ)对牟氏角毛藻生长、叶绿素荧光特性及基因组DNA甲基化水平的影响

以AsO2-和HAsO42-分别暴露处理牟氏角毛藻(Chaetocerosmulleri)研究As(Ⅲ、V)毒性作用,As(Ⅲ)浓度梯度为0、10、50、100、300和500 μmol/L,As(V)浓度梯度为0、30、60、120、300和600 μmol/L,分别在第1、3、7d取样,研究不同浓度的As(Ⅲ、V)...     

Morphological and molecular diagnoses of Polydora brevipalpa Zachs,1933(Annelida: Spionidae) from the shellfish along the coast of China

Shell-boring species Polydora brevipalpa Zachs, 1933 is redescribed based on morphological observations and molecular approach for future unambiguous identification. Genetic distance analyses showed that the interspecific polydorid variation (16.7%–25.6%) was at least 15 times higher than the intraspecific one (0.2%–0.9%) based on the cytochrome c oxidase subunit I (CO1) gene sequences of polydorids. However, 18S rDNA variation pattern demonstrated a rather narrow barcoding gap, with the interspecific polydorid variation (0.5%–5.6%) being very close to the intraspecific one (0.0%–0.4%). As such, the CO1 gene exhibited better DNA barcode for identification of polydorids than the 18S rDNA gene because of the sufficiently large barcoding gaps. Analysis of molecular variance results based on CO1 gene sequences showed that most variations in sequences (97.79%) lay within groups of adult worms and egg capsules rather than between them. This indicated that egg capsules from Crassostrea gigas (Thunberg, 1793) in Ningbo and Nantong were related to the adult worms from Patinopecten yessoensis (Jay, 1857) in Dalian, and both of them belonged to P . brevipalpa . This result was further supported by parsimony network analysis, which showed that egg capsules collected from diff erent localities and adult worms shared a single haplotype. This study was the first to report both P . brevipalpa infestation on C . gigas and to utilise the known CO1 sequences of the adult polydorids to validate morphologically unidentified egg capsules or early larvae. P . brevipalpa was most possibly brought to Chinese waters through transportation of Pa . yessoensis brood stock from Japan.     

逐步添加法制备单链环状DNA的影响因素探究

单链环状DNA在纳米技术、分子生物学和医药学等领域具有广泛的应用前景,但难以大量制备一直是制约其研究和应用的难题之一。本文针对一种高效大量制备单链环状DNA的方法-逐步添加法,系统地探究了逐步添加法中各主要条件对制备单链环状DNA的影响,确定了逐步添加法中的主要关键条件为:T4DNA连接酶Buffer浓度、单链DNA浓度、添加间隔时间、温度和Splint GC含量。以72nt的核酸链为例,使用逐步添加法将单链环状DNA的制备得率提高至99%,产量与常用的一步法相比提高至4.9倍。本研究为高效、大量制备单链环状DNA提供了指导,为以单链环状DNA为基础的研究奠定了基础。