基于涉案兽类12S rRNA基因的NCBI数据库序列可靠性分析

本研究以常用于动物种属鉴定的12S rRNA基因位点为研究对象,利用所测得的17种常见涉案兽类12S rRNA基因部分片段序列及NCBI数据库中下载的该物种DNA序列及其近缘物种DNA序列,构建系统进化树。根据进化树的聚类情况,判断NCBI数据库中的相关基因序列或物种名称的正确性,并对其中错误序列的登陆号进行标记,以防对后续涉案动物的准确鉴定造成影响。分别从17种常见涉案兽类(共26份样本)中提取线粒体DNA,并利用通用引物扩增线粒体DNA上的12S rRNA基因部分片段并进行测序分析。通过NCBI数据库的Blast比对功能,筛选出与本研究物种同源性由高到低的物种,并从NCBI基因数据库中下载此类近缘物种的12S rRNA基因序列共351条,利用MEGA7.0软件构建该物种及其近缘物种系统进化树。通过比对发现NCBI中登录号为KP202279等3个序列所对应物种拉丁名错误。登录号为AY184436等11个序列所对应物种拉丁名可能存在疑问。GenBank中某些物种拉丁名有同种异名现象。因此,NCBI数据库数据可靠性有待进一步验证,只能作为涉案物种鉴定的参考数据之一,可借助构建系统进化树等方法来确认其结果的准确性。     

基于Cytb基因的NCBI数据库序列可靠性分析

本研究以常用于动物种属鉴定的Cytb基因位点为研究对象,利用所测得的30种盗猎案件中常见的野生动物Cytb基因部分片段序列及NCBI数据库中下载的该物种序列及其近缘物种序列,构建系统进化树。根据进化树的聚类情况,判断NCBI数据库中的相关基因序列或物种名称的正确性,并对其中错误序列的登陆号进行标记,以防对后续涉案动物的准确鉴定造成影响。分别从30种常见涉案野生动物(共35份样本)中提取线粒体DNA,并利用通用引物扩增线粒体DNA上的Cytb基因部分片段并进行测序分析。通过NCBI数据库的Blast比对功能,筛选出与本研究物种同源性由高到低的物种,并从NCBI基因数据库中下载此类近缘物种的Cytb基因序列共482条,利用MEGA软件构建该物种的系统进化树。比对发现NCBI中登录号为DQ246798、KP202269、AY286434等3个序列所对应物种拉丁名错误。登录号为AY509634、AJ131639、AM072747等5个序列所对应物种拉丁名可能存在疑问。NCBI数据库数据可靠性有待进一步验证,只能作为涉案物种鉴定的参考数据之一,可借助构建系统进化树等方法来确认其结果的准确性。     

一个三物种生态系统模型

本文利用属性集合来定义物种,对于同一物种中的不同个体,各种属性所表现出的强度不同,导致了个体之间的差异性．对一个物种而言,它具有的某方面功能是由物种的不同属性体现于这方面的能力所共同决定的．本文对具有环状捕食结构的三物种构成的生态系统,以各物种的每个属性对和捕食逃逸能力的贡献方式为基础,将属性分为四类．讨论了四类属性随时间的演化规律．从所得的结果发现,随着时间的延伸,三物种可以稳定的共存;另外,对物种捕食和逃逸有利的属性在平均意义下是进化的,而对捕食和逃逸无作用的属性却无法被淘汰．     

关于iFlora创建工作框架的建议

iFlora是依据传统植物分类学及相关学科的研究基础,融入现代DNA测序技术,应用高速发展的信息、网络技术及云计算分析平台,收集、整合和管理植物物种相关信息,以建成智能物种鉴定和数据提取的开放应用系统（智能装备）。通过与该系统的双向交流,一方面,可以不断整合新的数据和技术充实iFlora的内容和功能;另一方面,可以通过该系统的多种鉴定途径实现快速、准确和方便的物种鉴定,获取所需物种的相关信息,满足专业机构和公众对物种和生物多样性的认知要求。本文重点介绍了构成iFlora的应用装置和支撑该装置的实物库（凭证标本、分子材料和DNA库）的建设及其重要性;阐述了构成iFlora各单元的高度整合和集成的特点,以及基于计算机技术的物种信息数字化和开放的云计算数据分析处理服务平台的枢纽作用;并讨论了iFlora创建过程所面临的困难和挑战,以及拟研发的智能装备的框架和应用前景。     

物种潜在分布地预测系统PSDS的设计与实现

本研究设计并实现了一个基于地理信息系统(GIS)的仅用物种已知分布点数据预测物种潜在分布地的PSDS系统.在这一系统中,通过层次聚类算法对物种已知分布点数据进行处理,减少了异常值对预测结果的影响,从而解决了环境包络模型预测结果过于乐观的问题,在物种已知分布数据较少时也能取得较好的结果.该系统实现了数据加载与导出、图层浏览与显示、生态因子分析与分布地预测、结果展示等功能,操作方便,简单易用.本文以白冠长尾雉(Syrmaticus reevesii)为例,根据4个省的少量已知分布点数据对其在国内的潜在分布地进行了预测,获得了较理想的结果,可为该物种的保护提供科学依据.     

中国重点保护物种名录、标准与管理

中国野生动物保护名录包括《国家重点保护野生动物名录》(简称《国家重点保护名录》)、《具有重要生态、科学和社会价值的陆生野生动物名录》》(简称《三有名录》)和地方重点保护野生动物名录(简称地方重点保护名录)。2017年《中华人民共和国野生动物保护法》修订实施后,《国家重点保护名录》修订工作提上日程。修订《国家重点保护名录》应明确该名录与《三有名录》之间的关系,前者要突出重点,体现保护优先和方便管理的原则,划分中央和地方的保护责任。建议依据物种的濒危属性、特有属性、稀有属性、珍贵属性以及管理属性来确定重点保护野生动物物种的级别。保护名录可以采取将整个属、整个科等较高的分类阶元集体列入原则(Principle of Clump Listing)。当一个亚种、一个种群有显著的进化潜力和确定的分布区时,也可以应用拆分列入原则(Principle of Splitting Listing),将其作为管理单位列入物种保护名单。此外,还应密切跟踪并及时更新物种分类法的变化、制订保护级别的判定标准、编写物种恢复计划指南、制定《国家重点保护名录》修订程序。建议为每一个重点保护物种制定相应的种群和生境恢复计划。根据珍稀濒危野生动物动态管理的需要,通过定期评估,及时对列入名录的物种进行升级、降级、删除或维持现有保护等级等处理。     

基于层次分析法的旗舰物种遴选方法

旗舰物种是保护生物学中一个广泛应用的概念, 用于获得公众对保护行为的支持, 在生物多样性保护领域发挥着重要作用。但目前尚未见量化分析遴选和确定旗舰物种的公开报道, 致使学术界对旗舰物种的定义和使用相对主观, 缺乏科学依据。本文对旗舰物种的定义进行了梳理, 探讨了旗舰物种的内涵, 确定了旗舰物种的属性, 制定了遴选标准和量化遴选方法, 以便读者更好地理解和运用这一概念。目前旗舰物种的定义仍然局限在其社会学属性, 作者建议今后应加强其生物生态学属性。作者认为除了公众的关注度和认可度之外, 旗舰物种还应具备以下3个生态生物学和社会文化特征: (1)物种在当地的濒危程度及生存现状; (2)物种在当地生态系统中的重要性; (3)物种在当地民众中的影响力和认可度。基于此, 本文确定了表征旗舰物种社会文化属性和生态生物学属性的8个要素, 基于层次分析法提出了一种量化的旗舰物种遴选方法。该方法综合上述8个要素进行评判和计算分值, 以塔吉克斯坦境内分布的14种大型濒危哺乳动物的生态生物学属性和社会文化影响力为基础, 描述基于层次分析法遴选塔吉克斯坦哺乳类旗舰物种的方法和过程, 最终依据每个备选物种所得分值高低排序, 得到塔吉克斯坦旗舰物种的优先备选物种。本文首次提出了一种量化遴选旗舰物种的方法, 期望今后可基于该方法开发更加合理的旗舰物种遴选模型和算法。     

甲虫群落构建研究进展

甲虫作为节肢动物中一个庞大的类群,具有繁简各异的生活习性,在生态系统中发挥极为重要的作用.甲虫群落构建是群落生态研究的重要内容之一,可揭示不同生态环境下生物多样性的形成与维持机制.现阶段对甲虫群落构建的研究主要通过物种的功能性状,或将系统发育结构与物种功能性状相结合的方法,对群落构建过程进行解析,用以判断主要的驱动因素...     

基于线粒体CO 1基因序列的DNA条形码在鲤科鲌属鱼类物种鉴定中的应用

本研究探讨了线粒体CO1基因作为DNA条形码对鲌属鱼类进行物种鉴定的可行性。研究中获得了鲌属4种鱼类共32个个体长度为816bp的CO1基因序列。利用MEGA软件计算鲌属鱼类种间及种内遗传距离,利用邻接法、最大简约法、最大似然法和Bayesian方法分别构建分子系统树。结果显示,鲌属鱼类的种间遗传距离显著大于种内遗传距离。在系统树中,鲌属鱼类每一物种的个体分别形成各自独立的分支。基于CO1基因的DNA条形码在识别鲌属鱼类物种方面和传统形态学基本一致,而且该基因可以探讨鲌属鱼类种间的系统发育关系。本研究表明以CO1基因作为鲌属鱼类DNA条形码进行物种鉴定具有一定的可行性。     

生态位模型的理论基础、发展方向与挑战

生态位模型是一个以生态位理论为基础的新兴研究领域.它通过采集研究对象的已知分布点及其相关的环境数据组成训练样本,利用数理统计或机器学习理论分析数据,构建特征函数表示物种在生态位空间的实际生态位.以生态位模型预测物种潜在分布地或计算物种间的生态位重叠等研究,在生态学、生物地理学和进化生物学研究中显得越来越重要.本文从生态位概念出发,详细解析了生态位模型的理论基础、相关的焦点争论、使用时的注意点以及可能的发展方向与面临的挑战,指出模型中要考虑人类活动对物种生态位的影响.希望本文所探讨的本领域最新的争论焦点能引起相关学者的关注与深入思考.     

On the concept of individual in ecology and evolution

Part of the art of theory building is to construct effective basic concepts, with a large reach and yet powerful as tools for getting at conclusions. The most basic concept of population biology is that of individual. An appropriately reengineered form of this concept has become the basis for the theories of structured populations and adaptive dynamics. By appropriately delimiting individuals, followed by defining their states as well as their environment, it become possible to construct the general population equations that were introduced and studied by Odo Diekmann and his collaborators. In this essay I argue for taking the properties that led to these successes as the defining characteristics of the concept of individual, delegating the properties classically invoked by philosophers to the secondary role of possible empirical indicators for the presence of those characteristics. The essay starts with putting in place as rule for effective concept engineering that one should go for relations that can be used as basis for deductive structure building rather than for perceived ontological essence. By analysing how we want to use it in the mathematical arguments I then build up a concept of individual, first for use in population dynamical considerations and then for use in evolutionary ones. These two concepts do not coincide, and neither do they on all occasions agree with common intuition-based usage.     

基因工程菌生产抗菌肽的研究进展

目前,利用基因工程菌生产抗菌肽,提供有效和稳定的方法是抗菌肽生产的热点之一。了解抗菌肽工程菌表达系统、生产量尤为重要,为此本文阐述了抗菌肽的生产方式,介绍了基因工程菌表达系统的种类、组成及特点,分析了基因工程菌生产抗菌肽的主要困难因素,并对近些年利用基因工程菌生产抗菌肽的进展进行了综述。     

Life With or Without Names

The terms ‘life’, ‘species’ and ‘individuals’ are key concepts in biology. However, theoretical and practical concerns are directly associated with definitions of these terms and their use in researchers’ work. Although the practical implications of employing definition of ‘species’ and ‘individuals’ are often clear, it is surprising how most biologists work in their field of study without adhering to a specific definition of life. In everyday scientific practice, biologists rarely define life. This is somewhat understandable: the majority of biologists accept the standard definition of life without exploring it, but this represents a bad attitude. In this essay, we update the concepts of life, species, and individuals in the light of the new techniques for massive DNA sequencing collectively known as high throughput DNA sequencing (HTS). A re-evaluation of the newest approaches and traditional concepts is required, because in many scientific publications, HTS users apply concepts ambiguously (in particular that of species). However, the absence of clarity is understandable. For most of the last 250 years, from Linnaeus to the most recent researches, identification and classification have been performed applying the same process. On the contrary, through HTS, biologists have become simply identifiers, who construct boundaries around the biological entities and do not examine the taxa at length, resulting in uncertainty in most readers and displeasure in traditional taxonomists. We organised our essay to answer a basic question: can we develop new means to observe living organisms?     

The sea urchin's siren

This issue of Developmental Biology features articles that constitute a new wave of insights into how a genome interacts with itself (as DNA) and with effectors-proteins and probably RNAs, collectively operating as a kind of "cis-trans" dualism. We learned a test for allelism in genetics class that bore that Latin name but now it comes as a new day for biological science-a welcome era in which a phenomenon as complex as development can be envisioned from principles of chemical binding energy and specificity. The buzzword (the term is just-as there is deserved buzz) is that the genome is hard-wired, in the sense that it has been shaped to both encode and react to a regulatory network, of which it is itself a part. I here review some of the milestones of embryology in which the sea urchin was the key player, segueing into the modern era in which this organism launched an entirely new intellectual construct of genome organization and gene expression during development. This essay also contains a number of personal perspectives as well as some views on the overall epistemological fabric of developmental biology. Like all of us, I am excited to see the S. purpuratus genome appear and heartily congratulate, by writing this essay, the trailblazers whose intellectual courage and persistence has brought us to this happy position.     

Perverting medical history in the service of "animal rights"

Scientists frequently disagree on the interpretation of data. Such disagreements follow an informal set of rules, where one assumes that the contestants are honestly engaged even though biases may cloud their minds. A new group of individuals with medical training operates under a different set of rules, however: any statement or argument may be used to support the animal rightists' contention that using animals to advance human medicine is wrong. These "medical scientists" pervert the scientific discourse in which most of us engage. Their fabrications are egregious. They take legitimate scientists' statements out of context, construct statements out of larger passages to twist arguments in their favor, and cite works that actually are contrary to their arguments for effect. This essay reveals the distortions by a number of such medically trained individuals that I and several colleagues have uncovered.     

Logical-Semantic Analysis and the Development of L.S. Vygotsky's Ideas About “Units” and “Elements” of Psychological Systems

Based on an analysis of L.S. Vygotsky's concepts of “units” and “elements” of psychological systems, this article highlights five of their attributes. It shows that these attributes are logically symmetrical, since in their wording they can be converted into one another by negation or by replacing some words with their opposites. This suggests that the concepts of the “unit” and “element” of a system are different poles of one theoretical construct of the activity of human psychology. Thus methods for the study of psychological systems by breaking them down into elements or by separating them into units can be seen as complementary. The article describes differences among the concepts of “unit,” “minimal unit,” and “cell” of a psychological system. It reviews several problems that are solvable using the “method of units,” as well as some concepts of the theory of psychological systems that are understood as holistic, conceptual, and active processes and/or results of human interaction with the world. Among the examples of such systems are “systems of psychological functions” (according to Vygotsky), as well as separate activities (according to A.N. Leontiev), human actions and operations (interactions with the world on the level of objects and mental or physical means). The “component” of a psychological system is defined as any “something” that in some sense belongs to or is included in human interaction with the world. A component that belongs to the system is called an “element” of it, but a component that is included in the functioning and development of the system is called a “part” of it. The article presents the mathematical and psychological foundation of these definitions. It identifies and discusses the substantial (independently existing) components of psychological systems and their attributes (properties and conditions). It describes the relationships between them using the bipolar theoretical constructs “part-element” and “substantial-attributive” component of a system.     

The visual ecology of fiddler crabs

With their eyes on long vertical stalks, their panoramic visual field and their pronounced equatorial acute zone for vertical resolving power, the visual system of fiddler crabs is exquisitely tuned to the geometry of vision in the flat world of inter-tidal mudflats. The crabs live as burrow-centred grazers in dense, mixed-sex, mixed-age and mixed-species colonies, with the active space of an individual rarely exceeding 1 m². The full behavioural repertoire of fiddler crabs can thus be monitored over extended periods of time on a moment to moment basis together with the visual information they have available to guide their actions. These attributes make the crabs superb subjects for analysing visual tasks and the design of visual processing mechanisms under natural conditions, a prerequisite for understanding the evolution of visual systems. In this review we show, on the one hand, how deeply embedded fiddler crab vision is in the behavioural and the physical ecology of these animals and, on the other hand, how their behavioural options are constrained by their perceptual limitations. Studying vision in fiddler crabs reminds us that vision has a topography, that it is context-dependent and pragmatic and that there are perceptual limits to what animals can know and therefore care about. For Mike Land     

Plant attributes determining the regional abundance of weeds on central European arable land

Aim Several recent studies have aimed to identify the biological, ecological and distributional attributes that determine the regional abundance of plant species. Here we aim to assess the relationships between regional abundance and species attributes in weeds on arable land. Location Czech Republic, central Europe. Methods The relationships between regional abundance and species attributes were studied with a data set of 381 weed species occurring on arable land in the Czech Republic. Regional species abundances were estimated from their occurrence frequency in vegetation plots distributed across the country. Using regression tree models, abundance was related to the biological traits, ecological indicator values, geographical distribution and habitat range of species. The models were calculated for the entire country and separately for weeds in cereals, root crops, lowlands and uplands. The effects of phylogenetic relatedness among species on their regional abundance were quantified and compared with the effects of species attributes. Results The results were similar for the whole data set and its particular subsets. Phylogeny explained 11.2–14.9% and species attributes 16.1–56.9% of the variation in regional abundance of weed species. Removal of the phylogenetic signal did not result in important changes in the effects of particular attributes. The most abundant species were those flowering in pre‐spring and early spring, adapted to low temperatures, relatively shade tolerant and with high nutrient requirements. The high regional abundance of these species positively correlated with their broad geographical (often circumpolar) distribution and broad habitat ranges. Main conclusions The regional abundance of weeds can, to some extent, be explained by their attributes. The most important attributes are those that enable weeds to grow and reproduce in the cool season when there is limited competition with crop plants, and those that are adaptations to growth in dense vegetation stands and highly productive habitats.     

Genetic diversity in three colonizing orchids with contrasting mating systems

Comparative studies on the genetic attributes of colonizing orchids with diverse mating systems are lacking in the literature. Eulophia sinensis, Spiranthes hongkongensis, and Zeuxine strateumatica are colonizing orchids that frequently occupy newly created habitats in Hong Kong. Mating system studies showed that E. sinensis is a self-compatible but pollinator-dependent outcrossing species, S. hongkongensis is a self-pollinating taxon, and Z srateumatica is apomictic. Population genetic attributes of these orchid species were investigated. Despite their contrasting mating systems, electrophoretic surveys revealed a striking lack of allozyme variation, both within and among populations, in all three species. However, gene duplications were evident in these species, due to their likely polyploid origins, The percentage of duplicate loci exhibiting "fixed heterozygosity" was 10, 21.4, and 20% in E. sinensis, S. hongkongensis, and Z. strateumatica, respectively. The genetic attributes of these orchids are compared to those found in other colonizing plant species.     

RNA self-ligation: from oligonucleotides to full length ribozymes

The RNA-world-theory is one possible explanation of how life on earth has evolved. In this context it is of high interest to search for molecular systems, capable of self-organization into structures with increasing complexity. We have engineered a simple catalytic system in which two short RNA molecules can catalyze their own ligation to form a larger RNA construct. The system is based on the hairpin ribozyme using a 2',3'-cyclophosphate as activated species for ligation. 2',3'-cyclic phosphates can be easily formed and occur in many natural systems, thus being superior candidates for activated building blocks in RNA world scenarios.