在线植物志: 网络时代分类学的方法和实践

全球气候变化、环境污染、资源被过度利用、外来物种入侵和生境丧失威胁着地球上物种的生存。分类学研究的主要任务就是在这些物种即将消失之前去发现、记录和认知它们。社会公众、政府决策部门和科学发展本身都对分类学提出了诸多需求。然而, 当前分类学所面临的困境包括认识上的误区、不科学的评价机制、研究队伍的萎缩以及陈旧的知识管理和发布模式等, 这些因素不仅阻碍了分类学的学科发展, 而且也制约了分类学家履行社会责任。利用现代的网络信息技术, 构建一个覆盖分类学研究工作流程、整合已有在线数据资源、满足分类学研究群体、项目和研究机构共同需求的分类学社区网络, 并最终实现分类学的终极目标--在线植物志, 将会极大地改善分类学的知识产出和应用环境, 提升它在当今科学技术发展条件下的竞争力, 使其真正成为一门21世纪的科学。     

The conservation imperative and setting plant taxonomic research priorities in South Africa

For more than a decade it has been internationally recognised that efforts should be made to remedy the concern that taxonomy is an endangered discipline in the grips of rapid decline. In acknowledgement of the perceived continuing marginalisation of taxonomy, the Darwin Declaration recognised the need to enhance the taxonomic capacity of members who are party to the CBD, and beyond. South Africa is one of the most biodiversity rich countries globally, and the unique and rich flora of the country brings with it a significant conservation imperative. Although the country, and southern African subregion for that matter, has a strong history of taxonomic endeavour, stretching back for over a century, it also suffers from a lack of human and other resources to adequately address its taxonomic needs. This inevitably calls for a process of priority-setting to ensure the wise use of available funding. As one example, it is shown that 1,009 indigenous South African plant taxa are regarded as Data Deficient for taxonomic reasons, following the completion of a recent comprehensive Red Listing exercise. Although not the only criterion to be considered when prioritising taxonomic research, efforts focused on these groups represent a significant opportunity for taxonomists to align their work with national priorities.     

The web and the structure of taxonomy

An easily accessible taxonomic knowledge base is critically important for all biodiversity-related sciences. At present, taxonomic information is organized and regulated by a system of rules and conventions that date back to the introduction of binomial nomenclature by Linnaeus. The taxonomy of any particular group of organisms comprises the sum information in the taxonomic literature, supported by designated type specimens in major collections. In this article, the way modern means of disseminating information will change the practice of taxonomy, in particular the Internet, is explored. Basic taxonomic information, such as specimen-level data, location of types, and name catalogues are already available, at least for some groups, on the Web. Specialist taxonomic databases, key-construction programs, and other software useful for systematists are also increasingly available. There has also been a move towards Web-publishing of taxonomic hypotheses, though as yet this is not fully permitted by the Codes of Nomenclature. A further and more radical move would be to transfer taxonomy completely to the Web. A possible model of this is discussed, as well as a pilot project, the "CATE" initiative, which seeks to explore the advantages and disadvantages of such a move. It is argued that taxonomy needs to forge better links with its user-communities to maintain its funding base, and that an important part of this is making the products of its research more accessible through the Internet.     

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.     

Impediments to taxonomy and users of taxonomy: accessibility and impact evaluation

There has been much discussion of the “taxonomic impediment”. This phrase confuses two kinds of impediment: an impediment to end users imposed by lack of reliable information; and impediments to taxonomy itself, which vary from insufficient funding to low citation rates of taxonomic monographs. In order to resolve both these types of impediment, taxonomy needs to be revitalized through funding and training taxonomists, as well as investing in taxonomic revisions and monographs rather than technological surrogates such as DNA barcoding.
© The Willi Hennig Society 2011.     

中国兽类分类与系统演化研究进展

中国兽类(即哺乳动物)种类繁多,对维持生态平衡发挥着重要的作用。自John R.Reeves于1829—1834年在我国广东开展兽类调查以来,近200年我国兽类分类及系统学研究取得了令世人瞩目的进步和发展。目前中国已知的兽类物种数已达686种,约占全世界兽类种数的10%,是世界上兽类物种多样性最丰富的国家之一。随着我国对生态环境保护的重视,生态环境日益改善,但全球气候变化、生境破碎化、人类活动增加及人兽共患重大疫情涌现等问题仍十分突出,兽类多样性调查及分类学研究的必要性越发明显。同时,兽类分类学这门古老而传统的学科也在不断引入各种新方法与技术,如整合分类学、标本数字化、模式标本测序、便携式测序技术及基于深度学习技术的物种识别鉴定等,分类学研究的成果及应用在近年得到了飞速发展。动物分类学作为传统的基础学科,是遗传学、生理学、生态学、医学、药学等现代生物学的基石。然而,由于学科特征和差异等原因,该学科近年来没有得到足够的重视,导致出现了学科萎缩和分类学人才后继无人的危机。因此,从国家层面对分类学、形态学等基础学科的人才培养、课题设置和资金投入等,予以特殊的政策支持,十分必要,也亟待解决。     

2020年后生物多样性保护需要建立新的资金机制

《生物多样性公约》第十五次缔约方大会(COP15)将评估全球生物多样性保护已有进展, 审议并通过“2020年后全球生物多样性框架”, 后者是实现2050愿景“与自然和谐相处”的关键, 有助于达成联合国可持续发展的目标。生物多样性资金机制现在是将来也是实施全球生物多样性保护行动计划的重要保证。根据《生物多样性公约》信息交换所的数据, 目前各缔约方每年对本国生物多样性保护的投资额度占其当年国内生产总值(GDP)的比例比较小。中国作为发展中国家, 2015年时生物多样性保护资金投入占GDP比例为0.255%, 在世界各国中处于比较高的水平。近年中国对生物多样性保护的投入连年增加, 2019年时已经达约0.6%。有研究表明, 目前全球每年生物多样性保护资金的缺口至少500亿美元, 未来十年还有更大的资金缺口, 而且当前已有生物多样性资金渠道比较单一, 并存在一些短板, 远远不能满足生物多样性保护行动的要求, 急需建立新的资金机制, 调动更多资源, 推动2030年生物多样性保护任务和目标的实现。《生物多样性公约》的资金机制可以与包括《联合国气候变化框架公约》在内的其他相关环境公约协同增效, 比如基于自然的解决方案将生物多样性保护与气候变化减缓等环境目标联系起来。中国作为COP15的东道国, 有积极协调磋商的责任, 力求在大会上推动形成一个新的资金机制, 即全球生物多样性保护基金, 为“2020年后全球生物多样性框架”的实施保驾护航。新的生物多样性保护资金机制将独立于现有的生物多样性保护资金机制, 具有多样化投资渠道并引入绩效评估机制, 将经费与任务目标关联, 提高资金的使用效率, 支持发展中国家的生物多样性保护行动。     

国家自然科学基金资助植物经典分类学的综述与思考

本文简单介绍了自2002年开始国家自然科学基金对植物经典分类学的资助情况,包括项目数、队伍培养、研究类群、标本采集和植物修订状况等,并针对项目执行过程中存在的主要问题,提出了几点建议。     

Taxonomy in the Kunming Institute of Botany (KIB): Progress during the past decade (2008-2018) and perspectives on future development

The development of new taxonomical theories and approaches, particularly molecular phylogenetics, has led to the expansion of traditional morphology-based taxonomy into the concept of "integrative taxonomy." Taxonomic knowledge has assumed greater significance in recent years, particularly because of growing concerns over the looming biodiversity crisis. Since its establishment in 1938, the Kunming Institute of Botany (KIB), which is located in Yunnan province in Southwest China, has focused attention on the taxonomy and conservation of the flora of China. For the forthcoming 80th anniversary of KIB, we review the achievements of researchers at KIB and their associates with respect to the taxonomy of land plants, fungi, and lichen. Major taxonomic advances are summarized for families of Calymperaceae, Cryphaeaceae, Lembophyllaceae, Neckeraceae, Polytrichaceae and Pottiaceae of mosses, Pteridaceae and Polypodiaceae of ferns, Taxaceae and Cycadaceae of gymnosperms, Asteraceae, Begoniaceae, Ericaceae, Euphorbiaceae, Gesneriaceae, Lamiaceae, Orchidaceae, Orobanchaceae, Poaceae, Theaceae and Urticaceae of angiosperms, Agaricaceae, Amanitaceae, Boletaceae, Cantharellaceae, Physalacriaceae Russulaceae, Suillaceae and Tuberaceae of fungi, and Ophioparmaceae and Parmeliaceae of lichens. Regarding the future development of taxonomy at KIB, we recommend that taxonomists continue to explore the biodiversity of China, integrate new theories and technologies with traditional taxonomic approaches, and engage in creative monographic work, with support from institutions, funding agencies, and the public.     

The taxonomist - an endangered race. A practical proposal for its survival

Background

Taxonomy or biological systematics is the basic scientific discipline of biology, postulating hypotheses of identity and relationships, on which all other natural sciences dealing with organisms relies. However, the scientific contributions of taxonomists have been largely neglected when using species names in scientific publications by not citing the authority on which they are based.

Discussion

Consequences of this neglect is reduced recognition of the importance of taxonomy, which in turn results in diminished funding, lower interest from journals in publishing taxonomic research, and a reduced number of young scientists entering the field. This has lead to the so-called taxonomic impediment at a time when biodiversity studies are of critical importance. Here we emphasize a practical and obvious solution to this dilemma. We propose that whenever a species name is used, the author(s) of the species hypothesis be included and the original literature source cited, including taxonomic revisions and identification literature - nothing more than what is done for every other hypothesis or assumption included in a scientific publication. In addition, we postulate that journals primarily publishing taxonomic studies should be indexed in ISI^SM.

Summary

The proposal outlined above would make visible the true contribution of taxonomists within the scientific community, and would provide a more accurate assessment for funding agencies impact and importance of taxonomy, and help in the recruitment of young scientists into the field, thus helping to alleviate the taxonomic impediment. In addition, it would also make much of the biological literature more robust by reducing or alleviating taxonomic uncertainty.     

蚁蛉科分类研究概况

回顾了世界蚁蛉科 2 0 0多年的分类研究历史。将科的分类研究进程依据年代先后分成 3个阶段 ,并对每个阶段分类研究的代表人物及所取得的成就做了介绍。以列表方式阐述了 1 899年以来所采用过的及目前普遍接受的分类系统。同时对世界蚁蛉科、属、种分布做了说明。最后介绍了中国蚁蛉科的分类研究     

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。     

《生物多样性公约》资金问题分析及对我国履约的启示

资金议题一直是《生物多样性公约》关注的热点, 资金机制和资源调动也一直是每届缔约方大会(COP)的常设议题。然而由于资金问题涉及各方政治意愿, 发达国家和发展中国家间存在较大分歧。中国作为最大的发展中国家和COP15主席国, 在资源调动中扮演着重要角色, 需要对资金问题开展更多研究。在这种背景下, 本文阐述了公共资金投入、资金使用效率与效力、对生物多样性有害的资金投入、利益相关方的参与等《生物多样性公约》资金问题重点要素; 分析了是否强调多渠道增资、是否建立新的资金机制、是否取消全部生物多样性有害补贴、具体筹资目标等谈判主要分歧; 提出了加大生物多样性财政资金投入、加强相关部门间资金协同管理, 利用各类金融工具撬动社会资本的生物多样性投入, 降低生物多样性损害风险、加强生物多样性信息披露, 充分发挥市场机制作用、创新融资路径等建议, 以期为中国生物多样性资源调动提供参考。     

杨属植物分类的研究进展和展望

自林奈建立杨属（Populus）以来,众多的学者对杨属的分类进行了研究,并建立了较多的分类系统。目前的国际杨属分类,总体上还停留在传统形态分类阶段,存在明显的地域和国别特征。尽管各国在主流上都采用“属—组—种”的分类阶元,但在种、亚种、变种的划分上,却存在很大的不同。中国和美国分别是细分派和聚合派的代表,两国的分类系统存在很大分歧,但各有优点和缺点。即使在国内,杨属分类也还有很多需要解决的问题。新兴的分子系统学研究,为杨属的分类修订提供了一些有益参考,但总体贡献不大。国际杨属分类的趋势和终极目标是建立基于系统发生的统一分类系统。这需要基于种群和综合物种概念,融合形态学、生态学、生物地理学、基因组生物信息学和进化生物学等的综合系统分类来实现。     

Classical and non-classical taxonomy: where does the boundary pass?

Rise of non-classical science during XX century had certain influence upon development of biological taxonomy. Scientific pluralism (especially normative naturalism of Laudan), contrary to positivist and early post-positivist treatments, made taxonomy acknowledged scientific discipline of its own right. The present state of some schools of taxonomy makes it possible to consider them as a part of non-classical science and constituting the non-classical taxonomy. The latter is characterized by the following most important features. Ontological substantiation of both classificatory approaches and particular classifications is requested which invalidates such formal approaches as nominalistic and phenetic (numerical) schools. This substantiation takes a form of content-wise background preferably causal models which include certain axioms and presumptions about taxonomic diversity being studied, together with its causes, and thus define initial conditions of classificatory procedures. From this viewoint, phylogenetic classificatory approach is the most developed part of non-classical taxonomy. The entire taxonomic diversity is structured into several aspects of different levels of generality, each being outlined by a particular consideration aspect. The latter makes personal knowledge constituting an irremovable part of any scientific statement about taxonomic diversity, thus opposition of "objectively" and "subjectively" elaborated classifications becomes vague. Interrelation of various species concepts corresponding to its different consideration aspects is described by uncertainty relation principle. Classificatory algorithms are to be compatible with the conditions of a background model to ensure particular classifications obtained by their means are interpretable within the same model: this is provided by the correspondence principle. Classification is considered as a taxonomic hypothesis, i.e. a conjectural judgement about structure of particular fragment of taxonomic diversity considered within given consideration aspect; wich is to be forwarded and tested according to certain rules. Recognition of different aspects of taxonomic diversity makes it "legal" to elaborate several classifications of equal status, each reflecting a particular aspect of a fixed fragment of that diversity. This viewpoint makes classical ideas of the "ultimate" Natural (whatever might be its definition) or the best reference systems futile. In general, any pretension of an approach to be "the best" in reflecting taxonomic divesrity is contr-productive. Instead, elaboration of particular spectra of complementary classifications becomes the main task of non-classical taxonomy which describes in sum the entire taxonomic diversity. So, not opposition but correct mutual interpretation of such classifications and uniting them into the comprehensive picture of taxonomic diversity become focal points of non-classical taxonomy.     

Isolation and Characterization of a cDNA That Encodes a Novel Proteinase Inhibitor I from a Tobacco Genetic Tumor

We have isolated a cDNA clone, designated GTI, by screeninga tobacco genetic tumor cDNA library with a tumor-specific "subtracted"cDNA probe. The cDNA contained the entire coding sequence fora 94-amino-acid polypeptide that exhibited significant homologyto members of the proteinase inhibitor I family from tomatoand potato. The predicted protein has a pre-sequence of 22 aminoacids but lacks a pro-sequence, unlike genes for proteinaseinhibitor I isolated to date. Furthermore, the protein encodedby GTI cDNA has a novel reactive site, having glutamine as theP₁ reactive residue. These results suggest that the GTI proteinis a novel member of the proteinase inhibitor I family. ThemRNA for GTI accumulated at a high level but only transientlyafter the wounding of tobacco plants. Thus, it appears thatthe GTI protein has a function that is related to the protectionof tissues against damage due to wounding. (Received July 22, 1992; Accepted November 3, 1992)     

Genomic taxonomy of vibrios

Background  

Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i. e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios.     

蜱类分类系统的变更

随着分子生物学技术在蜱类研究中的应用,及对蜱类系统发生的深入研究,蜱的分类及命名发生了很大变更。而中国在这一领域的研究还停留在20世纪90年代,分类系统过时。文章对中国曾经采用的蜱类分类系统与现今世界上普遍认可的分类系统进行了详细比较,以期引起注意,从而促进蜱类系统学及其他研究领域的发展。     

A review of criticisms of phylogenetic nomenclature: is taxonomic freedom the fundamental issue?

The proposal to implement a phylogenetic nomenclatural system governed by the PhyloCode), in which taxon names are defined by explicit reference to common descent, has met with strong criticism from some proponents of phylogenetic taxonomy (taxonomy based on the principle of common descent in which only clades and species are recognized). We examine these criticisms and find that some of the perceived problems with phylogenetic nomenclature are based on misconceptions, some are equally true of the current rank-based nomenclatural system, and some will be eliminated by implementation of the PhyloCode. Most of the criticisms are related to an overriding concern that, because the meanings of names are associated with phylogenetic pattern which is subject to change, the adoption of phylogenetic nomenclature will lead to increased instability in the content of taxa. This concern is associated with the fact that, despite the widespread adoption of the view that taxa are historical entities that are conceptualized based on ancestry, many taxonomists also conceptualize taxa based on their content. As a result, critics of phylogenetic nomenclature have argued that taxonomists should be free to emend the content of taxa without constraints imposed by nomenclatural decisions. However, in phylogenetic nomenclature the contents of taxa are determined, not by the taxonomist, but by the combination of the phylogenetic definition of the name and a phylogenetic hypothesis. Because the contents of taxa, once their names are defined, can no longer be freely modified by taxonomists, phylogenetic nomenclature is perceived as limiting taxonomic freedom. We argue that the form of taxonomic freedom inherent to phylogenetic nomenclature is appropriate to phylogenetic taxonomy in which taxa are considered historical entities that are discovered through phylogenetic analysis and are not human constructs.