基于高通量测序的表层水体纤毛虫多样性评估方法比较与优化

基于扩增子的高通量测序技术广泛应用于微型生物多样性的研究, 不同的测序手段和数据分析流程, 影响着微型生物多样性与群落结构的分析结果。本研究以易于形态鉴定的砂壳纤毛虫作为研究对象, 比较DNA测序、RNA测序和形态学方法检获的多样性和物种组成等, 探究序列分析流程中关键步骤: 嵌合体处理、可操作分类单元分析方法选择、合并相似分类单元以及去除稀有类群等对多样性结果的影响。研究结果显示无论基于DNA还是RNA的分子手段与形态学方法检获的主要物种基本一致, 与DNA测序相比, RNA测序检获的物种数少, 但差异不显著。基于97%以上相似度聚类和单核苷酸变异所得群落结构相似, 无显著差异; 且所有分析方法都能在一定程度上反映出自然界中不同类群的相对丰度。相较于单核苷酸变异和其他相似度阈值, 99%相似度下聚类所得多样性更为接近形态学结果。去除嵌合体和稀有类群(去除阈值: DNA测序0.05%; RNA测序0.07%), 可明显改善分子多样性虚高的问题。本研究为纤毛虫等真核微生物的分子多样性研究提供了科学的数据分析流程, 对未来真核微生物多样性研究具有指导意义。     

BOOK REVIEWS

Book Reviewed in this article: Unfairly Structured Cities . Blair Badcock Religion and Rural Revolt . Janos M. Bak and Gerhard Benecke The Industrial Geography of Canada . Anthony Blackbourn and Robert G. Putnam The Cuban-American Experience, Culture, Images, and Perspectives. Thomas D. Boswell and James R. Curtis Quaternary Paleoclimatology . R. S. Bradley Development and Crisis in Brazil, 1930–1983 . Luiz Bresser Pereiras Centres of Origin in Biogeography . John C. Briggs Analytical Urban Geography . Martin Cadwallader Geomorphology . Richard J. Chorley , Stanley A. Schumm, and David E. Sugden South Africa: The Impact of Past Geographies . A. J. Christopher The Geography of Underdevelopment. A Critical Survey . D. K. Forbes Health Care in Developing Countries . Wilbert M. Gesler Place to Grow Old: The Meaning of Environment in Old Age . Stephen M. Golant The Emerging Marine Economy of the Pacific . Chennat Gopalakrishnan An Introduction to Agricultural Geography . David B. Grigg The Soviet Union: A Geographical Study . G. Melvyn Howe Geographical Aspects of Health: Essays in Honour of Andrew Learmonth . N. D. Mc Glashan and J. R. Blunden Physical Geography: A Landscape Appreciation . Tom L. Mc Knight Mountain Experience. The Psychology and Sociology of Adventure. Richard G. Mitchell Jr . Systematic and Regional Biogeography. Stanley A. Morain The Economic Transformation of American Cities. T. J. Noyelle and T. M. Stanback , Jr . Normal Accidents: Living With High-Risk Technologies. Charles Perrow Vanishing Farmland: A Legal Solution for the States. Sarah E. Redfield Applied Methods of Regional Analysis: The Spatial Dimensions of Development Policy. Dennis A. Rondinelli Urbanization in Romania. A Geography of Social and Economic Change Since Independence. Per Ronnas Statistical Techniques in Geographical Analysis. Gareth Shaw and Dennis Wheeler The Granite Garden: Urban Nature and Human Design. Anne Whiston Spirn Political Geography: Recent Advances and Future Directions. Peter Taylor and John House Geographia y Medio Ambiente. Manuel Valenzuela -Rubío Nãgara and Commandery: Origins of the Southeast Asian Urban Traditions. Paul Wheatley The Common Fisheries Policy of the European Community. Mark Wise Geography and Gender. Women and Geography Study Group of the IBG Technological Hazards. D. J. Zeigler , J. H. Johnson , S. D. Brunn     

Unique vs. non-unique stratal geometries: Relevance to sequence stratigraphy

The sequence stratigraphic architecture includes a complex array of stratal geometries with different degrees of stratigraphic significance. The ‘non-unique’ variability of the sequence stratigraphic framework (i.e., stratal geometries which are not diagnostic for the definition of systems tracts and bounding surfaces) is irrelevant to the workflow of sequence stratigraphy. What is relevant is the observation of the ‘unique’ stratal geometries that are diagnostic for the definition of units and surfaces of sequence stratigraphy. In downstream-controlled settings, these unique stratal stacking patterns relate to the forced regressive, normal regressive, and transgressive shoreline trajectories. Multiple controls interact during the formation of each type of stacking pattern, including accommodation, sediment supply, and the energy of the sediment-transport agents. This interplay explains the non-unique variability, but does not change the unique criteria that afford a consistent application of sequence stratigraphy. The distinction between unique and non-unique stratal geometries is critical to the sequence stratigraphic methodology. Failure to rationalize the non-unique variability within the context of unique stratal geometries is counterproductive, and obscures the simple workflow of sequence stratigraphy. This is the case with uncalibrated numerical modeling, which may overemphasize non-unique or even unrealistic stratigraphic scenarios. While useful to test the possible controls on stratigraphic architecture, modeling requires validation with real data, and plays no role in the sequence stratigraphic methodology.     

在三亚湾环境下四种方法在五种造礁石珊瑚上移植效果的比较

珊瑚移植一直被认为是增加退化珊瑚礁上珊瑚数量的重要手段之一。为了调查多种珊瑚移植方法和不同珊瑚种类的移植效果,我们选择了已严重退化并仍面临着人类和自然环境胁迫的三亚鹿回头珊瑚礁作为移植地,对5种珊瑚共902个断枝利用4种方法进行了移植。在移植后的10个月,移植珊瑚的存活率为45.5%。移植方法对于不同珊瑚种类具有不同效果,但没有一种方法能够对所有珊瑚的移植效果产生促进作用。虽然对于叶状蔷薇珊瑚（Montipora foliosa）和风信子鹿角珊瑚（Acropora hyacinthus）来说,适合的移植方法能够减缓其死亡速率,但并不能改变其死亡趋势。叶状蔷薇珊瑚和风信子鹿角珊瑚的移植个体呈现出高死亡率和明显的存活组织面积下降,而扁枝滨珊瑚（Porites andrewsi）和丛生盔形珊瑚（Galaxea fascicularis）死亡率和组织部分死亡率则优于前两者。扁枝滨珊瑚和丛生盔形珊瑚仅在一种移植方法中出现了存活组织面积明显增长。鹿角杯形珊瑚（Pocillopora damicornis）是移植珊瑚中唯一一种在所有移植方法上都呈现珊瑚平均存活面积增长的种类。实验结果说明在受到高度胁迫的海域进行珊瑚移植很难取得满意效果,珊瑚种类的选择对胁迫环境下的珊瑚移植效果具有决定性影响,而移植方法只能在部分程度上改善移植效果,但无法弥补鹿回头环境压力对敏感种类胁迫造成的影响。在鹿回头珊瑚礁需首先治理对珊瑚造成胁迫的因子,再进行珊瑚移植,并应优先考虑移植环境耐受性高的珊瑚种类。     

Voice Under Scrutiny: Feminist Methods,Anticolonial Responses,and New Methodological Tools

“Giving voice” to participants has been an important element of qualitative feminist research projects in geography. In this article, I explore scholarship that has questioned qualitative research's reliance on voice, arguing that implicit connections between voice, authenticity, and empowerment are beginning to be unpacked, particularly by scholars engaged in anticolonial work. I draw on anticolonial scholarship to build on and extend feminist debates centered on voice and participation. Feminist attention to voice must be situated within the colonial frameworks and histories of social science research. Scholarship focused on ongoing settler colonial relationships highlights methods both for cautiously proceeding with and consciously refusing incorporating voice within qualitative research. I draw on anticolonial approaches to frame research decisions, voice, and the ethical and methodological dilemmas of its use.     

Evaluation of the N2 flux approach for measuring sediment denitrification

Direct gas chromatographic measurement of denitrification rates via N₂ fluxes from aquatic sediments can avoid some of the artifacts and complexities associated with indirect approaches and tracer techniques. However, measurement protocols have typically been determined based upon initial results or previous studies. We present a process-level study and simulation model for evaluating and optimizing N₂ gas flux approaches in closed chamber incubations. Experimental manipulations and simulations of both artificial and natural sediments were used to conduct sensitivity analyses of key design parameters in N₂ flux measurements. Experimental results indicated that depletion of labile organic matter during the long incubations required by common protocols (for diffusive off-gassing of porewater N₂) may result in underestimates of denitrification rates in some systems. Simulations showed that the required incubation time was primarily a function of sediment thickness. The best approach found to minimize incubation time and reduce errors was to select the minimum sediment thickness necessary to include the entire depth distribution of nitrification–denitrification for a particular sediment system. Attempts to increase measurement sensitivity and shorten incubation times by reducing the headspace thickness to 1–2 cm generally cause denitrification to be underestimated by 3–13% for gas headspaces, and up to 80% for water headspaces. However, errors were negligible with gas and water headspace thicknesses of 10 cm and 15 cm, respectively. Anaerobic cores to control for non-denitrification N₂ fluxes shortened incubation time, but introduced artifacts in sediments with extensive macrofaunal irrigation.     

地洼学说发展中的若干问题探讨

本文从科学哲学的角度.结合具体的科学发展历史,对地洼学说的理论结构和发展纲领.对历史因果论大地构造学的建立和壳体概念的提出与阐述.从科学方法论和科学理论发展的历史規律方面.探讨了地洼学说发展中的若干问题:概念方法.假说方法在地洼学说发展中的应用问题,地洼学说中的内核和保护层问题;地洼学说发展中的“范式”与“科学共同体”的建立问题;以及地洼学说发展的模式问题。     

2000年以来浙江省海洋产业结构演化特征与态势

浙江省是海洋经济大省,但并非强省,近10年来浙江海洋经济一直位居全国第4或第5位。海洋经济发展,深受其产业结构及布局影响。以浙江海洋产业结构演化特征为研究内容,运用2001～2010年海洋经济统计数据,采用数理统计分析与演化经济地理学方法探讨浙江海洋产业结构演化的路径依赖、创造与锁定等的具体表现。研究表明:(1)浙江海洋产业部门立足资源与区位优势趋向于多样化、产业结构渐趋合理化,但海洋产业科技含量较低、新兴海洋产业发展缓慢;(2)浙江海洋渔业、海洋交通运输业、滨海旅游业、海洋船舶工业、海洋盐业的演化过程呈现鲜明的资源依赖性和历史路径惯性作用,而海水利用业、海洋电力、海洋生物医药产业则是内生技术研发与应用发展的典范;(3)浙江部分海洋产业路径锁定解除模式与窗口选择不合时宜,如海洋交通运输业与海洋盐业等。因此,破解浙江海洋产业结构演化过程路径锁定的最佳模式是以经济社会环境综合改善集聚海洋人才,形成本土研发创新能力,攻克海洋产业核心技术与管理创新。     

石油地质动力学的内涵与展望

石油地质动力学的本质特征是在现代地质理论基础之上，应用数学、物理学、化学和生物学等理论和方法，借助先进的计算机和实验测试、模拟技术，定量地研究沉积盆地油气生、运、储、聚和保的机制、速率和过程。石油地质动力学研究的核心问题有两个：一是沉降作用，二是流体压力系统形成与演化，成藏动力是石油地质动力学研究的纽带。石油地质动力学现行研究方法可分为盆地动力学、石油地质动力学（狭义）和地质作用过程动力学，重点介绍了成岩过程动力学的研究方法及当今研究的前沿领域，即热流体与有机／无机成岩作用。最后，笔者展望了石油地质动力学研究在我国那些具有多旋回叠合性含油气盆地的发展和应用前景。     

地质过程动力学体系、研究层次及认识论

本文根据作者个人的观点讨论了地质过程动力学的本质特征,根据地质过程动力学广泛的研究对象和研究内容归纳了地质过程动力学的分支体系,并依据地质过程动力学的不同研究水平和研究方法把地质过程动力学划分成3个不同的层次,分别讨论了各层次动力学的研究方法。最后,作者讨论了有关地质过程动力学研究中经常遇到的几个认识问题,期望对地质过程动力学研究起到推动作用。