一种简易塑化动物标本的制作方法

在改变传统标本制作及保存方法上进行了尝试研究,形成一种由水溶性塑料聚乙二醇(PEG)处理标本的方法。经该方法制作处理的标本无需其他防腐剂如甲醛、苯酚等溶液浸泡,且能防霉、防虫。研究结果表明此方法在标本制作及保存方面具有明显的实用价值。     

单核苷酸多态性的研究及其生物学意义

单核苷酸多态性(SNP)是基因组中发生频率最高的变异种类.目前数据库内的SNP数量已经超过了9 000 000个,人体的许多表型差异,以及对药物或疾病的易感性等,都可能与SNP有关.研究SNP可促进人们对基因组结构、基因的进化历史及疾病发生根源的了解.SNP是种群遗传分析、疾病发生机理和药物研发等领域的重要研究对象.目前,针对SNP研究所建立的数据库和高效、精确、方便操作的工具,对于展现SNP在引领遗传分析、疾病诊治等领域发展方面的重要性具有很高的利用价值.     

中国蝙蝠新记录--马氏菊头蝠

通过对广西防城港市和陆川县采集到的蝙蝠标本进行鉴定,发现7只马氏菊头蝠( Rhinolophus marshalli, Thonglongya 1973)中国蝙蝠新记录。本文在与模式标本数据进行比较的基础上,对该批标本进行了详细测量和描述。     

用于GWAS结果后续研究的PBA方法简介

自提出全基因组关联研究(genome-wide association study,GWAS)设想以来,在人类复杂疾病和水稻农艺性状关联研究方面,GWAS已得到广泛运用。但作为一种典型的单标记研究方法,GWAS不能检测小效应的遗传变异,而稀有变异间的联合效应往往与表型密切相关,因此,需对GWAS结果进行深入的数据挖掘。基于通路的分析方法(pathway-based analysis,PBA)就是利用基因功能、生物代谢通路等相关信息建立的对GWAS结果进行二次挖掘的方法。该方法能从GWAS结果挖掘出与性状、疾病相关联的通路及具有相同功能的基因集等数据,从而获得更多的遗传信息。现对PBA的出现、计算方法和相关软件进行简要综述,以期为人们进行通路分析提供参考。     

城市生态智慧管理系统的生态系统服务评估功能与应用

开展生态系统服务评估已经成为国土空间功能管治、城市治理、生态产品价值实现等工作中的先行基础动作。生态系统服务的类型和模型方法多,数据需求复杂,传统基于多学科软件开展生态系统服务评估的工作模式知识和技术门槛较高、效率低。当前专业的生态系统服务评估软件多为美国从业人员开发,对我国的数据构成和本地化参数适应性有限。介绍了我国自主开发的生态系统分析软件（城市生态智慧管理系统,IUEMS）的主要功能和应用情况,并将其的生态系统服务评估功能与InVEST、ARIES等国外主流软件在操作逻辑、评估模型、数据取得、空间精度、界面交互五个方面进行了对比。     

RSAP分子标记技术在园艺植物研究中的应用

限制性位点扩增多态性(RSAP)是一种基于PCR的新型植物分子标记技术,具有操作简便、结果稳定、效率较高的特点。该技术以植物基因组上广泛分布的限制性位点位为靶标,通过独特的引物设计和PCR扩增程序,无需限制性酶切环节,只要一个简单的PCR,即可产生基于植物限制性位点的多态性标记。阐述了RSAP的原理与流程,对该技术的优势和应用情况做了总结,并对其前景进行了展望。     

植物标本标签设计的原则及R程序包herblabel

植物标本是分类学、生态学和分子生物学最重要的凭证之一。标本的采集和鉴定信息需清晰、准确、美观地展示和保存于标本标签中, 不能有歧义以及拼写错误。在标签的制作过程中, 数据输入的方式要简单、直接, 标签文件生成过程中最好能自动分析错误, 且在打印之前要便于修改和调整。本文探讨了打印植物标本标签的若干原则以及注意事项, 并介绍了用R语言编写的herblabel程序包生成植物标本标签以及鉴定标签的过程。herblabel程序包基于Darwin Core和CVH5.0数据交换标准, 可快速批量生成几种样式的RTF标签, 且标签简洁、美观, 易于编辑。herblabel程序包具有检查地点完整程度, 学名拼写和接受状态, 科、属在APG等新系统下的对应关系等功能, 可有效减少数据录入过程中产生的错误。此外, 本程序包在打印标签时使用的是基于Darwin Core标准保存的标本数据库, 不仅方便统计和管理, 也可以直接用于全球生物多样性信息网络(GBIF)数据共享或者数字植物标本馆的建设。该程序包可显著提高植物标本馆标本制作、管理和信息录入的工作效率, 减轻工作人员的负担, 并在植物生物多样性编目中发挥重要作用。     

利用SSR分子标记解析遗传学三大规律

分离规律、自由组合规律和连锁规律被称为遗传学三大规律,是认识生物遗传和变异的基础。一般教学中,主要通过对分离世代性状的表型分离特性进行观察和统计分析,是一种基于表型的分析,而利用位于同一染色体和不同染色体上的微卫星(Simple sequence repeats,SSR)分子标记,在分离世代的基因型数据及PCR扩增产物带型的分析,可以从核酸水平上比较直观地解释遗传规律,提高教学效果,加深学生对遗传规律的认识。     

黑叶猴外形整体结构的研究

根据黑叶猴(Presbytis francoisi)解剖标本的测量数据,用几何方法绘制出整体外形结构图;用R聚类分析结果找出了所测变量之间的相互关系;Q聚类和三维空间模式结构展示了黑叶猴外形整体结构与蜘蛛猴、食蟹猴、长臂猿、大猩猩和黑猩猩之间的相互关系。结果表明,在所测的23项变量中,由5个小聚类组成:与个体大小相关的变量、与前肢结构相关的变量、与后肢结构相关的变量、与颅骨结构相关的变量和臀部结构。在这些变量中,臀部宽与其他变量表现了极弱的相关关系。黑叶猴的外形整体结构与其他几种灵长类比较,更接近于食蟹猴和长鼻猴,其次接近于蜘蛛猴。因此从外形整体结构相似性分析,黑叶猴的运动与食蟹猴、长鼻猴和蜘蛛猴具有某些相似处。     

结构域相互作用数据库的产生、发展与应用

结构域是进化上的保守序列单元,是蛋白质的结构和功能的标准组件．典型的两个蛋白质间的相互作用涉及特殊结构域间的结合,而且识别相互作用结构域对于在结构域水平上彻底理解蛋白质的功能与进化、构建蛋白质相互作用网络、分析生物学通路等十分重要．目前,依赖于对实验数据的进一步挖掘和对各种不同输入数据的计算预测,已识别出了一些相互作用/功能连锁结构域对,并由此构建了内容丰富、日益更新的结构域相互作用数据库．综述了产生结构域相互作用的8种计算预测方法．介绍了5个结构域相互作用公共数据库3DID、iPfam、InterDom、DIMA和DOMINE的有关信息和最新动态．实例概述了结构域相互作用在蛋白质相互作用计算预测、可信度评估,蛋白质结构域注释,以及在生物学通路分析中的应用．     

Reliable,verifiable and efficient monitoring of biodiversity via metabarcoding

To manage and conserve biodiversity, one must know what is being lost, where, and why, as well as which remedies are likely to be most effective. Metabarcoding technology can characterise the species compositions of mass samples of eukaryotes or of environmental DNA. Here, we validate metabarcoding by testing it against three high‐quality standard data sets that were collected in Malaysia (tropical), China (subtropical) and the United Kingdom (temperate) and that comprised 55,813 arthropod and bird specimens identified to species level with the expenditure of 2,505 person‐hours of taxonomic expertise. The metabarcode and standard data sets exhibit statistically correlated alpha‐ and beta‐diversities, and the two data sets produce similar policy conclusions for two conservation applications: restoration ecology and systematic conservation planning. Compared with standard biodiversity data sets, metabarcoded samples are taxonomically more comprehensive, many times quicker to produce, less reliant on taxonomic expertise and auditable by third parties, which is essential for dispute resolution.     

In search of a functional flora—towards a greater integration of ecology and taxonomy

Large-scale biodiversity informatics projects will not properly address the needs of one important potential user group. Ecologists do not have ready access to datasets which allow them to assign plant species to functional types. We believe that information technology has developed sufficiently to allow taxonomists and ecologists to work together to address this need and develop specimen databases to combine taxonomic data with ecological and ecophysiological information so that this information will be assigned to the correct taxon in the future. Digital images provide a rapid and economical method of vouchering specimen data, reducing the need to store physical vouchers in herbaria.     

生物多样性国际研究态势分析

生物多样性研究是综合性和高度交叉性的跨学科研究领域,是1997年底Science周刊上预测的1998年及近期的6个重大科学热点之一。检索1986—2008年间SCIE文献数据库中关于生物多样性的研究论文(article,proceedings paper和review),利用Thomson Data Analyzer(TDA)分析工具和Aureka分析平台进行数据挖掘。分析表明,该研究涉及多个学科领域,近年来在生态学领域的论文数量增加最多,而生物多样性保护、进化生物学、生物化学与分子生物学方面的论文增长速度较快。生物多样性研究越来越重视全球变化和人类社会对生物多样性的影响,DNA技术和基因工程等先进技术在生物多样性研究和保护中的作用也更加突出。     

The contribution of small collections to species distribution modelling: A case study from Fuireneae (Cyperaceae)

The recent and rapid digitization of biodiversity data from natural history collection (NHC) archives has enriched collections based data repositories; this data continues to inform studies of species' geographic distributions. Here we investigate the relative impact of plant data from small natural history collections (collections with < 100,000 specimens) on species distributional models in an effort to document the potential of data from small NHCs to contribute to and inform biodiversity research. We modelled suitable habitat of five test case species from Fuireneae (Cyperaceae) in the United States using specimen records available via the Global Biodiversity Information Facility and that of data ready to mobilize from two regional small herbaria. Data were partitioned into three datasets based on their source: 1) collections-based records from large NHCs accessed GBIF, 2) collections-based records from small NHCs accessed from GBIF, and 3) collections-based records from two small regional herbaria not yet mobilized to GBIF. We extracted and evaluated the ecological niche represented for each of the three datasets by applying dataset occurrences to 14 environmental factors, and we modelled habitat suitability using Maxent to compare the represented distribution of the environmental values among the datasets. Our analyses indicate that the data from small NHCs contributed unique information in both geographic and environmental space. When data from small collections were combined with data from large collections, species models of the ecological niche resulted in more refined predictions of habitat suitability, indicating that small collections can contribute unique occurrence data which enhance species distribution models by bridging geographic collection gaps and shifting modelled predictions of suitable habitat. Inclusion of specimen records from small collections in ongoing digitization efforts is essential for generating informed models of a species' niche and distribution.     

遥感用于森林生物多样性监测的进展

随着物种和栖息地的丧失,全球范围的生物多样性保护已经成为迫切的需要。航空航天技术的迅猛发展使遥感成为能提供跨越不同时空尺度监测陆地生态系统生物多样性的重要工具,这方面的研究在欧美等国已经有了小范围的开展,在国内刚刚起步。国外关于生物多样性遥感探测的方法基本有3种:1.利用遥感数据直接对物种或生境制图,进而估算生物多样性;2 .建立遥感数据的光谱反射率与地面观测物种多样性的关系模型;3.与野外调查数据结合直接在遥感数据上进行生物多样性指数制图。研究表明,物种直接制图法只能应用于较小的范围;生境制图的方法,应用广泛,技术相对成熟,研究范围局限于几百公里的范畴,但不能获取生境内部的多样性信息。光谱模型技术目前正处于探索阶段,对于植被复杂、生物多样性高的地域,具有较大的应用潜力。在遥感数据上直接进行生物多样性制图在加拿大已经得到了应用。     

Mobilizing and integrating big data in studies of spatial and phylogenetic patterns of biodiversity

The current global challenges that threaten biodiversity are immense and rapidly growing. These biodiversity challenges demand approaches that meld bioinformatics, large-scale phylogeny reconstruction, use of digitized specimen data, and complex post-tree analyses (e.g. niche modeling, niche diversification, and other ecological analyses). Recent developments in phylogenetics coupled with emerging cyberinfrastructure and new data sources provide unparalleled opportunities for mobilizing and integrating massive amounts of biological data, driving the discovery of complex patterns and new hypotheses for further study. These developments are not trivial in that biodiversity data on the global scale now being collected and analyzed are inherently complex. The ongoing integration and maturation of biodiversity tools discussed here is transforming biodiversity science, enabling what we broadly term “next-generation” investigations in systematics, ecology, and evolution (i.e., “biodiversity science”). New training that integrates domain knowledge in biodiversity and data science skills is also needed to accelerate research in these areas. Integrative biodiversity science is crucial to the future of global biodiversity. We cannot simply react to continued threats to biodiversity, but via the use of an integrative, multifaceted, big data approach, researchers can now make biodiversity projections to provide crucial data not only for scientists, but also for the public, land managers, policy makers, urban planners, and agriculture.     

Geospatially structured biodiversity information as a component of a regional biodiversity clearing house

To function effectively, the international biodiversity Clearing HouseMechanism (CHM), based on the Convention on Biological Diversity (CBD), needs tobe rooted at the regional and local levels. This article presents an example ofhow stakeholders of regional data and information can be encouraged to formnetworks linked to national biodiversity focal points (NFPs). We pay specialattention to exploiting the geospatial properties of biodiversity data andinformation, and demonstrate how data and information can best be filtered,classified and labelled to facilitate geographically based information retrievalon the Internet. The geocodability of bibliographic reports proved to be poor,indicating an urgent need to reconsider the geographical properties ofbiodiversity information under production. Also, it is useful to utilisenetworking processes with information from fields other than biodiversity wheninitiating the network. Finally, we present and discuss problems of integrityand interoperability of data, and also the process of biodiversity informationproduction from the point of view of general information theory and innovationsoffered by modern information technology.     

全球标本数字化建设及共享发展趋势

标本数字化建设是生物多样性保护和利用的重要工作基础,通过标本数据的整合分析,在生物分类学、生态学、生物工程、生物保护、粮食安全、生物多样性评估、教学教育和人类社会活动等方面提供数据支撑。为了了解全球标本数字化建设工作的现状以及数据共享的策略与技术发展趋势,该文分别调查梳理了北美洲、南美洲、欧洲、非洲、亚洲和大洋洲地区的标本数字化和平台建设情况,对标本数据共享现状和趋势从数据使用协议、新技术新方法和公众科学等方面进行了对比和分析,并为中国国内的标本数字化工作提出了工作建议,包括:(1)加强标本数字化建设、管理和动态更新方面的协同机制建设,确保实物资源和数字化资源信息同步;(2)加强数据整理和发布,促进数据质量的提升,充分开放数据使用协议,减少数据使用的阻碍;(3)加强对新技术的学习和引入,特别是开源软件、机器学习和人工智能技术的应用,能够在标签快速识别、自动鉴定和属性数据提取等方面发挥作用;(4)加强区域和国际合作,推动数据的整合应用;(5)推动公众科学项目发展,促进野外采集、室内整理、在线纠错、数据产品研发等工作的开展。     

海洋保护区管理与保护成效评估的方法与进展

全球物种多样性的持续下降使得生物多样性保护面临巨大挑战, 海洋生物多样性的保护任务尤其艰巨。海洋保护区是保护生物多样性的有效方式之一, 如何对其成效进行评估是当前研究热点。然而, 目前针对海洋保护区的评估体系较少, 而且评估指标多侧重于管理成效。近年来随着全球生物多样性监测网络和数据库的建立, 以及多种新技术(如遥感、声呐系统、卫星追踪、基因组学等)在海洋生物多样性监测中的应用, 使得从生态系统到基因水平的多层次连续监测成为可能。基于此, 建议未来我国海洋保护区成效评估应在充分利用新技术方法的基础上, 加强长期科学监测, 建立并完善生物多样性监测数据库和信息共享机制, 发展跨学科的综合保护成效评估体系, 加强基于生物多样性监测的保护成效评估。     

Improving biodiversity monitoring

Effective biodiversity monitoring is critical to evaluate, learn from, and ultimately improve conservation practice. Well conceived, designed and implemented monitoring of biodiversity should: (i) deliver information on trends in key aspects of biodiversity (e.g. population changes); (ii) provide early warning of problems that might otherwise be difficult or expensive to reverse; (iii) generate quantifiable evidence of conservation successes (e.g. species recovery following management) and conservation failures; (iv) highlight ways to make management more effective; and (v) provide information on return on conservation investment. The importance of effective biodiversity monitoring is widely recognized (e.g. Australian Biodiversity Strategy). Yet, while everyone thinks biodiversity monitoring is a good idea, this has not translated into a culture of sound biodiversity monitoring, or widespread use of monitoring data. We identify four barriers to more effective biodiversity monitoring in Australia. These are: (i) many conservation programmes have poorly articulated or vague objectives against which it is difficult to measure progress contributing to design and implementation problems; (ii) the case for long‐term and sustained biodiversity monitoring is often poorly developed and/or articulated; (iii) there is often a lack of appropriate institutional support, co‐ordination, and targeted funding for biodiversity monitoring; and (iv) there is often a lack of appropriate standards to guide monitoring activities and make data available from these programmes. To deal with these issues, we suggest that policy makers, resource managers and scientists better and more explicitly articulate the objectives of biodiversity monitoring and better demonstrate the case for greater investments in biodiversitymonitoring. There is an urgent need for improved institutional support for biodiversity monitoring in Australia, for improved monitoring standards, and for improved archiving of, and access to, monitoring data. We suggest that more strategic financial, institutional and intellectual investments in monitoring will lead to more efficient use of the resources available for biodiversity conservation and ultimately better conservation outcomes.