基于16S rRNA基因的三种枝吻纽虫系统发育关系分析

测定了湛江枝吻纽虫（Dendrorhynchus zhanjiangensis）、中华枝吻纽虫（Dendrorhynchus sinensis）及疣多枝吻纽虫（Polydendrorhynchus papillaris）线粒体16S rRNA基因部分片段序列,结合从GenBank下载的其他纽虫序列,对它们之间的系统发育关系进行了分析.26个中华枝吻纽虫个体共检测到长度为467-468 bp的9个单倍型,5个湛江枝吻纽虫个体的长度均为469 bp,共检测到3个单倍型,2个疣多枝吻纽虫个体的长度均为474 bp,共享1个单倍型;核苷酸序列A、T、G、C的含量相似,碱基组成均表现出AT含量偏倚,即AT含量明显高于GC含量.中华枝吻纽虫9个单倍型之间的遗传距离和湛江枝吻纽虫3个单倍型之间的遗传距离均为0.002 1-0.004 3;而3种枝吻纽虫16S rRNA基因序列彼此之间的遗传距离却均超过0.24,显示它们之间的遗传差异特别大,分子系统树（NJ）的拓扑结构也显示,3种枝吻纽虫没有聚成1支,而是各自成支,结果支持3种枝吻纽虫分别为独立有效物种.中华枝吻纽虫与2种脑纹纽虫（Cerebratulus lacteus、C.marginatus）的遗传距离分别为0.154、0.169,明显低于与其同属的湛江枝吻纽虫的遗传距离（0.242）,表明中华枝吻纽虫与前两者的亲缘关系相对较近,而与后者的亲缘关系相对较远;在NJ树上,中华枝吻纽虫没有与湛江中华枝吻纽虫聚为1支,而是其9个单倍型聚为1支后,与2种脑纹纽虫（C.lacteus、C.marginatus）聚为1支,且有高达94%的支持率,这表明枝吻纽虫属（Dendrorhynchus）并非单系,也提示将中华枝吻纽虫划入脑纹纽虫属（Cerebratulus）会更合适.     

条斑紫菜叶状体DNA的高效制备

探索优化研磨条斑紫菜叶状体提取DNA的条件,建立一套简单、快速、高效的高通量研磨破碎方法。钢珠研磨80s时的破碎效果与液氮研磨破碎效果相近,因此选用80s作为研磨时间。利用2种样品材料(干燥和新鲜)、4种研磨介质(钢珠Φ2.3mm、陶瓷珠Φ1mm、石英砂0.270~0.707mm和玻璃珠Φ0.5mm)、3个研磨介质体积梯度(0.1、0.2和0.3mL)设计研磨实验。结果发现,钢珠的破碎效果最好,玻璃珠的破碎效果最差;石英砂和玻璃珠组研磨干燥材料所得DNA完整性最好,4种研磨介质研磨新鲜材料所得DNA出现了降解,钢珠和陶瓷珠研磨干燥材料所得DNA降解最严重;研磨介质的体积对样品的破碎程度、DNA得率和DNA质量没有显著性影响;4种研磨介质研磨干燥和新鲜材料所提DNA的纯度均较高。80s的研磨实验中显示,钢珠组能有效的破碎干燥和新鲜材料,获得DNA的纯度和得率都比较高,但是DNA出现了降解。在此基础上设置了0.2mL钢珠研磨干燥和新鲜材料5~40s的时间梯度。实验结果显示,钢珠在5~40s时均能有效的破碎干燥、新鲜2种样品材料。干燥材料研磨5~40s时,DNA有明显的主条带,DNA得率随着研磨时间的延长有所增加,DNA质量较好,且能用于限制性内切酶酶切实验;新鲜材料研磨5~40s时,DNA有明显的主条带,DNA得率没有显著性差异,DNA质量较好,也能用于限制性内切酶酶切实验。所以本文认为破碎干燥和新鲜2种样品材料制备高质量条斑紫菜DNA的最佳条件为:研磨介质为0.2mL钢珠、研磨速度为6 800r/min、研磨时间为5s。     

Zooplankton community analysis in the Changjiang River estuary by single-gene-targeted metagenomics

DNA barcoding provides accurate identification of zooplankton species through all life stages. Single-gene-targeted metagenomic analysis based on DNA barcode databases can facilitate longterm monitoring of zooplankton communities. With the help of the available zooplankton databases, the zooplankton community of the Changjiang (Yangtze) River estuary was studied using a single-gene-targeted metagenomic method to estimate the species richness of this community. A total of 856 mitochondrial cytochrome oxidase subunit 1 (cox1) gene sequences were determined. The environmental barcodes were clustered into 70 molecular operational taxonomic units (MOTUs). Forty-two MOTUs matched barcoded marine organisms with more than 90% similarity and were assigned to either the species (similarity>96%) or genus level (similarity<96%). Sibling species could also be distinguished. Many species that were overlooked by morphological methods were identified by molecular methods, especially gelatinous zooplankton and merozooplankton that were likely sampled at different life history phases. Zooplankton community structures differed significantly among all of the samples. The MOTU spatial distributions were influenced by the ecological habits of the corresponding species. In conclusion, single-gene-targeted metagenomic analysis is a useful tool for zooplankton studies, with which specimens from all life history stages can be identified quickly and effectively with a comprehensive database.     

DNA barcoding assessment of green macroalgae in coastal zone around Qingdao,China

An assessment with assistance of DNA barcoding was conducted on green macroalgae in coastal zone around Qingdao, China, during the period of April–December, 2011. Three markers were applied in molecular discrimination, including the plastid elongation factor tufA gene, the internal transcribed spacer (ITS) region of the ribosomal cistron and rubisco large subunit gene 3′ regions (rbcL-3P). DNA barcoding discriminated 8 species, excluding species of genus Cladophora and Bryopsis due to failures in amplification. We ascertained and corrected 4 species identified by morphological methods for effectively assisting the classification. The gene tufA presented more advantages as an appropriate DNA marker with the strongest amplification success rate and species discrimination power than the other two genes. The poorest sequencing success largely handicapped the application of ITS. Samples identified by tufA and rbcL as Ulva flexuosa were clustered into the clade of U. prolifera by ITS in the neighbor-joining tree. Confusion with discrimination of the complex of U. linza, U. procera and U. prolifera (as the LPP complex) still existed for the three DNA markers. Based on our results, rbcL is recommended as a preferred marker for assisting tufA to discriminate green macroalgae. In distinguishing green-tide-forming Ulva species, the free-floating sample collected from the green tide in 2011 was proved to be identical with U. prolifera in Yellow Sea for ITS and rbcL genes. This study presents a preliminary survey of green macroalgae distributed in the coastal area around Qingdao, and proves that DNA barcoding is a powerful tool for taxonomy of green macroalgae.     

中部太平洋大眼金枪鱼种群遗传结构的初步研究

大眼金枪鱼是世界最重要的渔业资源之一,经济价值较高,捕捞压力的加大使中部太平洋大眼金枪鱼过度捕捞程度愈发严重。开展种群遗传结构研究将为大眼金枪鱼资源的可持续利用与开发提供科学依据。本文以取自中西太平洋和中东太平洋共182尾大眼金枪鱼个体为研究对象,分析研究其线粒体DNA控制区第一个高变区（the first hypervariable region,HVR-1）457bp的序列,共发现115个变异位点,定义了178种单倍型。序列多样性分析结果显示8个采样点核苷酸多样性在0.03074-0.04362间,单倍型多样性在各个采样点都较高,变动范围在0.996-1.000之间;分子方差分析显示99.97%的遗传变异性来自于种群内;群体间的高基因交流值Nm和低分化指数Fst揭示中东太平洋与中西太平洋群体间基因交流频繁,不存在显著的遗传分化。     

磁力仪探头之间安全距离的实验与认识

为了加强对磁法勘察工作的管理和保证工作质量,为适应科学技术的进步和发展,特别是磁法仪器的不断提升和更新,适时修订相关的技术规程或者工作规范是十分必要的.修订技术规程或者工作规范亦应该契合实际,一是规定明确,二是在保证质量的前提下便于生产单位参照执行.笔者就《地面高精度磁测技术规程》的关于仪器噪声检测时探头的安全间距规定进行探讨,结合相关的磁测技术规定和教科书的要求及专门的试验结果,通过专门实验进行分析讨论,引用实例进行说明,认为并建议对上述规定进行修订.     

石榴子石反应边及其地质意义——以大兴安岭第四纪火山岩为例

大兴安岭第四纪火山岩(包括诺敏河火山区和哈拉哈河-绰尔河火山区)地幔包体中含有少量石榴子石,普遍发育矿物反应边.根据显微照片和BSE图像特征,石榴子石反应边可分为3类:①冠冕状石榴子石反应边,包裹在石榴子石矿物外部,具有一期或者多期反应的特征,厚度通常为0.1～1 mm,反应边矿物组合为Opx+Glass、Cpx+Gl...     

玻璃质壳类底栖有孔虫卷转虫属Ammonia spp.的DNA保存方式和提取效能比较研究

对有孔虫的DNA进行有效保存及提取是开展有孔虫分子鉴定工作的前提。本研究以探索适合玻璃质壳类底栖有孔虫的DNA保存及提取方法为目的,以中国近海优势属——玻璃质类底栖有孔虫卷转虫属(Ammonia spp.)为模式生物,考察不同温度(20—120°C,间隔10°C)烘干、冷冻(–20°C、–80°C,有水、无水)以及脱氧胆酸钠裂解液(Na deoxycholate,简称DOC)处理(含和不含EDTA)保存有孔虫DNA方法,同时进行了DOC裂解液法和Guanidine裂解液法对Ammonia spp.DNA提取效能的比较。结果显示,烘干保存法中20°C组和30°C组显著优于40°C组(P0.05);冷冻保存法中无水组显著优于有水组(P0.05);DOC裂解液保存法各组间无显著差异(P0.05)。三种保存方法综合效果表现为冷冻组显著优于烘干组和裂解液组(P0.05);两种DNA提取方法的提取效果都很好,但DOC法更廉价且操作简便。本文给出了一套适用于玻璃质壳类有孔虫的DNA保存和提取的优化方案。     

中华钩线虫的DNA条形码研究及分类意义探讨

海洋线虫是海洋底栖生物中数量上最丰富的类群,在海洋生态系统中起着重要的作用。对海洋线虫进行种类鉴定是线虫研究中最重要的工作之一。目前,海洋线虫的鉴定主要采用形态学的分析方法,但是这种方法往往费时费力,对于如此丰富的物种,急需新的鉴定方法。作者以黄海潮间带自由生活线虫优势种——中华钩线虫(Oncholaimus sinensis)为例,在形态学分类的基础上,将DNA条形码技术引入线虫的鉴定中,探讨了线粒体细胞色素C氧化酶第一亚基(mt COI)基因序列、28S r DNA序列的D2D3区以及18S r DNA序列的部分序列作为DNA条形码在中华钩线虫中的适用性。结果表明,18S r DNA序列可作为该种线虫的DNA条形码,为海洋线虫的DNA条形码研究提供了很好的借鉴。目前,利用DNA条形码技术对海洋线虫进行鉴定的报道在国内还属空白,本研究将是海洋线虫分类学研究的很好补充。同时,对于了解该海域海洋线虫多样性及群落分布格局,开展海洋环境监测,进而对海洋的底质环境状况进行健康评价具有十分重要的科学意义。     

Using palaeoenvironmental DNA to reconstruct past environments: progress and prospects

Palaeoenvironmental DNA (PalEnDNA) is defined as ancient DNA (aDNA) originating from disseminated genetic material within palaeoenvironmental samples. Sources of PalEnDNA include marine and lake sediments, peat, loess, till, ice, permafrost, palaeosols, coprolites, preserved gut contents, dental calculus, tephras, and soils as well as deposits in caves/rockshelters and at archaeological sites. PalEnDNA analysis provides a relatively new tool for Quaternary and archaeological sciences and its applications have included palaeoenvironmental and palaeodietary reconstructions, testing hypotheses regarding megafaunal extinctions, human–environment interactions, taxonomic studies, and studies of DNA damage. Because PalEnDNA samples comprise markedly different materials, and represent wide‐ranging depositional and taphonomic contexts, various issues must be addressed to achieve robust, reproducible findings. Such issues include climatic and temporal limitations, the biological origin and state (free versus bound) of PalEnDNA, stratigraphic reliability, sterile sampling, ability to distinguish modern from aDNA signals, DNA damage and PCR amplification, DNA extraction methods, and taxonomic resolution. In this review, we provide a non‐specialist introduction to the use of PalEnDNA for Quaternary and archaeological researchers, assess attributes and limitations of this palaeoenvironmental tool, and discuss future prospects of using PalEnDNA to reconstruct past environments.