近代鸟类分类与系统发育研究进展

简要综述了宏观和微观领域的鸟类分类学研究进展.宏观领域介绍了传统形态分类学、数值分类学和支序分类学,结合鸣声分析强调支序分类学的应用.微观领域介绍了Sibley分类系统和近年来出现的主要基于mtDNA的鸟类系统学研究.通过对大量研究工作的分析提出该领域今后应进行综合性研究.     

根瘤菌多样性和系统发育研究的多相分类体系及其进展

近年来对新的根瘤菌资源的不断发掘及现代分子生物学技术的发展和应用使根瘤菌分类研究有了突破性进展。多相分类通过综合获取信息,多种方法相互印证、互为补充,推进了根瘤菌的表型、遗传型和系统发育三方面的发展,从而较全面地反映根瘤菌的生物多样性特征,是根瘤菌多样性研究工作中常常采用的技术手段。文中主要阐述了根瘤菌多相分类体系中的主要方法及现代根瘤菌系统发育地位的研究和进展。     

基于Web的中国昆虫科级鉴别分类系统InsectID的设计与开发

详细介绍了国内首个昆虫科级鉴别分类网络系统InsectID(见http://insectx.3322.org)的设计思路、各组成部分的结构与功能,讨论了开发过程中分类检索表的转化与再现、系统分类树与特征解释机制的实现等关键问题。该系统具有分类单元全面、信息可靠、鉴定简单、扩充性强、更新便捷等诸多优点,是昆虫分类研究与教学的有力工具,也适用于其他生物分类系统的构建。     

世界蚜虫分类研究进展

本文综述了世界蚜虫分类研究进展。内容包括形态分类、细胞分类、生物化学分类以及化石研究等,并以M.L.Sharma的文献目录为基础,对世界蚜虫分类研究报告篇数进行统计。结果表明:世界各国蚜虫分类研究进展极不平衡,美国、加拿大、日本及欧洲的一些国家包括荷兰、丹麦、瑞典、捷克、波兰、德国等其α分类任务基本完成,印度也进展较快,离完成α分类任务为期不远。苏联欧洲部分也已基本完成,亚洲部分和中国尚有大量α级分类工作有待完成。     

放线菌的分子分类

在放线菌分类学研究中,最初是根据形态特征、生理生化特征等表观分类学特征进行研究。随着分子生物学的飞速发展,放线菌的分类鉴定亦从传统的表型分类进入到各种基因型分类水平。分子分类在放线菌分类研究中起到越来越重要的作用,目前放线菌的分子分类研究主要包括:G Cmol%测定、DNA杂交、核酸结构分析以及DNA指纹图谱分析等方面。     

Integrative taxonomy,or iterative taxonomy?

The recently introduced term ‘integrative taxonomy’ refers to taxonomy that integrates all available data sources to frame species limits. We survey current taxonomic methods available to delimit species that integrate a variety of data, including molecular and morphological characters. A literature review of empirical studies using the term ‘integrative taxonomy’ assessed the kinds of data being used to frame species limits, and methods of integration. Almost all studies are qualitative and comparative – we are a long way from a repeatable, quantitative method of truly ‘integrative taxonomy’. The usual methods for integrating data in phylogenetic and population genetic paradigms are not appropriate for integrative taxonomy, either because of the diverse range of data used or because of the special challenges that arise when working at the species/population boundary. We identify two challenges that, if met, will facilitate the development of a more complete toolkit and a more robust research programme in integrative taxonomy using species tree approaches. We propose the term ‘iterative taxonomy’ for current practice that treats species boundaries as hypotheses to be tested with new evidence. A search for biological or evolutionary explanations for discordant evidence can be used to distinguish between competing species boundary hypotheses. We identify two recent empirical examples that use the process of iterative taxonomy.     

植物病原棒形细菌的分类研究进展

植物病原棒形细菌从棒杆菌属中独立出来之后,对于其中各菌分类地位的确立一直有较多争议。近年来已分别归入棒形杆菌属（Clavibacter）、短小杆菌属（Curtobacterium）、节杆菌属（Arthrobacter）、红球菌属（Rhodococcus）和拉氏杆菌属（Rathayibacter）5个属中。但此后又有人提出有些属中仍有异质性。这些分类上的变化主要是由于分类手段逐渐由传统的形态学分类方法向分子生物学方法和多相分类法过度。新的方法还在不断的完善之中。此外,植物病原棒形细菌分类系统的完善还有赖于植物病理学和微生物学家等多学科科学家的合作。     

用主成分分析法分析金翅夜蛾亚科各性状对分类的重要性和性状变异方向

本文在“金翅夜蛾亚科的数值分类研究”的基础上用主成分分析的结果对金翅夜蛾亚科分类的性状做进一步分析,说明各性状对分类的重要性和性状的变异方向,并对用协方差矩阵和相关矩阵进行的主成分分析结果进行比较,说明对本问题（分类指标全是定性指标）适宜用协方差矩阵做主成分分析。     

Numerical taxonomy: criticisms and critiques: Presidential address to the Systematics Association, November 1970

Some recent criticisms and critiques of numerical taxonomy are reviewed, together with some of its present shortcomings. It is pointed out that most of the problems are equally severe for orthodox taxonomy, and many of them can only be investigated by numerical techniques. The reasons for the general success of numerical methods in bacterial classification are discussed. Besides bringing deeper insights into taxonomy as a whole, numerical taxonomy is entering a new and heuristic phase, which includes potential applications to the study of evolution.     

中国植物分类及标本采集史简述

植物分类学是一门古老的科学,其发展也受到了社会历史变革的深刻影响。该文通过对我国植物分类学研究和发展史进行简要回顾,根据人们对植物分类学科的认识程度以及社会重大历史事件等,将我国植物分类的发展史大体分为原始、古代、近代和现代4个阶段,并对各阶段进行了简要说明。植物标本是植物分类研究最基本和最重要的凭证材料,因此我国的植物标本采集史也见证了植物采集人员在我国植物分类学研究发展的历史过程中所付出的血汗、泪水甚至生命。植物资源的保护和种质资源的收集和保存正日益成为我国生态文明建设的主要内容,在新时代生物多样性保护的背景下,植物分类学和植物分类研究人员将会发挥更重要的作用,为我国的生物多样性保护提供更加有力的支撑。     

Concepts of rational taxonomy

The problems are discussed related to development of concepts of rational taxonomy and rational classifications (taxonomic systems) in biology. Rational taxonomy is based on the assumption that the key characteristic of rationality is deductive inference of certain partial judgments about reality under study from other judgments taken as more general and a priory true. Respectively, two forms of rationality are discriminated--ontological and epistemological ones. The former implies inference of classifications properties from general (essential) properties of the reality being investigated. The latter implies inference of the partial rules of judgments about classifications from more general (formal) rules. The following principal concepts of ontologically rational biological taxonomy are considered: "crystallographic" approach, inference of the orderliness of organismal diversity from general laws of Nature, inference of the above orderliness from the orderliness of ontogenetic development programs, based on the concept of natural kind and Cassirer's series theory, based on the systemic concept, based on the idea of periodic systems. Various concepts of ontologically rational taxonomy can be generalized by an idea of the causal taxonomy, according to which any biologically sound classification is founded on a contentwise model of biological diversity that includes explicit indication of general causes responsible for that diversity. It is asserted that each category of general causation and respective background model may serve as a basis for a particular ontologically rational taxonomy as a distinctive research program. Concepts of epistemologically rational taxonomy and classifications (taxonomic systems) can be interpreted in terms of application of certain epistemological criteria of substantiation of scientific status of taxonomy in general and of taxonomic systems in particular. These concepts include: consideration of taxonomy consistency from the standpoint of inductive and hypothetico-deductive argumentation schemes and such fundamental criteria of classifications naturalness as their prognostic capabilities; foundation of a theory of "general taxonomy" as a "general logic", including elements of the axiomatic method. The latter concept constitutes a core of the program of general classiology; it is inconsistent due to absence of anything like "general logic". It is asserted that elaboration of a theory of taxonomy as a biological discipline based on the formal principles of epistemological rationality is not feasible. Instead, it is to be elaborated as ontologically rational one based on biologically sound metatheories about biological diversity causes.     

VirusTaxo: Taxonomic classification of viruses from the genome sequence using k-mer enrichment

Classification of viruses into their taxonomic ranks (e.g., order, family, and genus) provides a framework to organize an abundant population of viruses. Next-generation metagenomic sequencing technologies lead to a rapid increase in generating sequencing data of viruses which require bioinformatics tools to analyze the taxonomy. Many metagenomic taxonomy classifiers have been developed to study microbiomes, but it is particularly challenging to assign the taxonomy of diverse virus sequences and there is a growing need for dedicated methods to be developed that are optimized to classify virus sequences into their taxa. For taxonomic classification of viruses from metagenomic sequences, we developed VirusTaxo using diverse (e.g., 402 DNA and 280 RNA) genera of viruses. VirusTaxo has an average accuracy of 93% at genus level prediction in DNA and RNA viruses. VirusTaxo outperformed existing taxonomic classifiers of viruses where it assigned taxonomy of a larger fraction of metagenomic contigs compared to other methods. Benchmarking of VirusTaxo on a collection of SARS-CoV-2 sequencing libraries and metavirome datasets suggests that VirusTaxo can characterize virus taxonomy from highly diverse contigs and provide a reliable decision on the taxonomy of viruses.     

Multiple objective ant colony optimisation

Multiple Objective Optimisation is a fast growing area of research, and consequently several Ant Colony Optimisation approaches have been proposed for a variety of these problems. In this paper, a taxonomy for Multiple Objective Ant Colony Optimisation algorithms is proposed and many existing approaches are reviewed and described using the taxonomy. The taxonomy offers guidelines for the development and use of Multiple Objective Ant Colony Optimisation algorithms.     

Taxonomy workbench.

At advanced stages of working with user-defined protein and gene sequence collections, it is frequently necessary to link these data to the taxonomic tree and to extract subsets in accordance with taxonomic considerations. Since no general automatic tools had been available, this was a tedious manual effort. Our taxonomy workbench allows processing of sequence sets, mapping of these sets onto the taxonomic tree, collection of taxonomic subsets from them and printing of the whole tree or some part of it. As a side effect, the system enables queries to and navigation within the taxonomy database. AVAILABILITY: An implementation of the taxonomy workbench is accessible for public use as a www-service at http://mendel.imp.univie.ac.at/taxonomy/. Software components for the command-line and for the www-version are available on request. CONTACT: Georg.Schneider@nt.imp.univie.ac.at; Frank.Eisenhaber@nt.imp.univie.ac.at SUPPLEMENTARY INFORMATION: Documentation for the taxonomy workbench can be accessed at http://mendel.imp.univie.ac.at/taxonomy/help.html.     

云南医学革螨数值分类研究

以云南省57种医学革螨作为分类单元,以形态特征为主列出60项分类性状特征来探讨云南省医学革螨不同属和种的亲缘关系。运用SPSS 11.5 统计软件中的系统聚类分析和主成分分析,对57种医学革螨进行了数值分类分析。结果显示：57种医学革螨划分为厉螨科（La elapidae）、寄螨科（Parasitidae）、皮刺螨科（Dermanyssidae）、赫刺螨科（Hirstionyssidae）和裂胸螨科（Aceosejidae）5个类群。赫刺螨属和棘刺螨属从厉螨科中分离出来另立为赫刺螨科,柏氏禽刺螨归入了皮刺螨科而不是巨刺螨科。分类结果与传统形态分类结果基本一致,因而认为数值分类能比较客观地反映医学革螨各分类阶元的分类地位与亲缘关系。     

'Integrative taxonomy' then and now: a response to Dayrat (2005)

Deep misunderstandings still besiege taxonomy after more than 200 years of fruitful output. It has been asserted in this journal that taxonomy should be integrative and conform to a series of restrictive guidelines. We show that taxonomy has been integrative for most of its history although, in our sense, integrative does not mean the indiscriminate pooling of any source of data. The guidelines proposed are not founded in good scientific rationale and can have, if followed, a detrimental effect not only on taxonomy, but also on biology as a whole.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 93 , 211–216.     

Building on Bedrock: William Steel Creighton and the Reformation of Ant Systematics, 1925–1970

Ideas about the natural world are intertwined with the personalities, practices, and the workplaces of scientists. The relationships between these categories are explored in the life of the taxonomist William Steel Creighton. Creighton studied taxonomy under William Morton Wheeler at Harvard University. He took the rules he learned from Wheeler out of the museum and into the field. In testing the rules against a new situation, Creighton found them wanting. He sought a new set of taxonomic principles, one he eventually found in Ernst Mayr's Systematics and the Origin of Species. Mayr's ideas tied together a number of themes running through Creighton's life: the need for a revised taxonomy, the emphasis on fieldwork, and the search for a new power center for ant taxonomy after Wheeler died. Creighton's adoption of Mayr's ideas as part of his professional identity also had very real implications for his career path: field studies required long and intensive studies, and Creighton would always be a slow worker. His method of taxonomy contrasted sharply not only with Wheeler's but also with two of his younger colleagues, William L. Brown and E. O. Wilson, who took over Wheeler's spot at Harvard in 1950. The disputes between these men over ant taxonomy involved, in addition to questions of technical interest, questions about where and how best to do taxonomy and who could speak withthe most authority. Creighton's story reveals how these questions are interrelated. The story also reveals the importance of Mayr's book for changes occurring in taxonomy in the middle of the twentieth century. This revised version was published online in July 2006 with corrections to the Cover Date.