我国古植物命名中若干值得重视的问题——兼述维也纳法规中有关的规定

根据2006年发表的新版国际植物命名法规(维也纳法规)的有关规则和条款,讨论我国古植物命名中一些值得重视的和存在的问题,着重在分类单元名称的合格发表、模式指定以及拉丁属、种名称构成和性别等几个方面.文中也介绍了新法规中对古植物形态分类单元(morphotaxa)定义的改变和相关规则的更动情况,以及有关在学位论文和电子版文档中发表分类单元名称等新规则.文后附有古植物命名的一些重要规则生效的日期和相关说明.     

国际植物命名法规中的术语介绍

现今,国际上已普遍接受国际植物命名法规(International code of botanical nomenclature)作为管理植物学(包括藻类学和真菌学)科学命名的规则。该规则由历届国际植物学大会的命名法分会会议修订,因而每六年出版一次修订版。最新版的维也纳法规     

中国药用真菌名录及部分名称的修订

近年来,我国对药用真菌的研究和利用越来越重视,相关报道逐年增加。针对有些种类鉴定有误、拉丁学名使用没有严格遵守最新国际植物命名法规、命名人缩写不规范等问题,作者系统考证了我国药用真菌的名称,共收录473种,对每种名称按新近的研究成果和最新命名法规(维也纳法规)进行了订正,对过去的错误报道或不存在的名称进行了修正,将曾报道的、但应作为其他种的同物异名者列在其正名之后,所有名称定名人的缩写全部按国际植物命名法规的要求加以规范化。每种名称之后还列举了该种的主要药用功能或价值,并引证了主要参考文献。     

中国食用菌名录

作者系统地考证了我国食用菌的名称,排除了过去报道中的187个名称,同时新增了82个名称,本文共收录中国食用菌966个分类单元,包括936种、23变种、3亚种和4变型。对每个名称按新近的研究成果和最新命名法规(维也纳法规)进行了订正,将曾报道的、但应作为其他种的同物异名者列在其正名之后,所有名称定名人的缩写全部按国际植物命名法规的要求加以规范化。     

扫描生命条码 鉴定物种身份

自从林奈创立双命名法以来的250年中,170多万种生物已经被分类及命名。然而,这只是地球上估计现存的1000万～1亿种生物中的很小一部分,按照这个分类速度推测下去,还需要1500年～1．5万年的时间才能将所有的分类鉴定工作完成。     

浅评当今植物系统学中争论的三个问题——并系类群、谱系法规和系统发育种概念

一般来讲,进化学派承认分支学派对系统学的研究作出了有意义的贡献,如应用分支分析方法重建系统发育,应用共有衍征确定分类群之间的分支关系以及应用外类群方法来判断性状的极性等,都对系统学的方法有所改进。但分支学派的致命缺点是拒绝接受并系类群。我们属于进化学派,认为并系类群是可以接受的。例如,根据分子资料分析,Zabelia属可以包括于Abelia属内。Zabelia属不但在花粉上和Abelia属不同,可能由于它占有了新的生态位,获得了新的特征,如叶柄基部膨大两两联合,并宿存以保护腋芽。有理由认为它们应独立成属,并不由于Zabelia属从Abelia属分出而使后者成为一个并系类群而把它们合并。分支学派的一些学者认为生物名称作为交流的工具和生物信息储存系统应有明晰的、唯一的和稳定的特性。但具等级的林奈命名系统并不具有这些特性来命名分支和种。最后,PhyloCode被提出。PhyloCode对分支的命名方法有3种,即分支结点定义、分支基干定义和衍征定义。我们认为林奈命名系统作为传媒系统在生物学界的应用已近250年,若要废弃它而采用PhyloCode,必然会在命名方面引起一片混乱。但我们并不是说PhyloCode的拥护者所提出的建议一无是处,我们建议他们宜继续进行研究。由于应用生物学种概念于植物界产生了许多问题,因此多为植物系统学家所抛弃。分支学派的兴起,推动了系统发育种概念的提出。该概念基于3个特征,即自征、区别特征和基本排它,因此分别命名为自征种概念、特征种概念和谱系种概念。事实上,目前大多数植物系统学家仍然应用着形态–地理学种概念,但我们在划分种时,必须有尽可能多的资料,特别是要将传粉、繁育系统、分子系统学资料和形态学资料结合起来。     

国际生物命名法规的协调与统一

根据林奈双名制原则,不同的生物学科曾先后制定出相应的命名法规,使各自学科的生物命名规范化。现行的国际生物命名法规有5个,即动物命名法规、植物命名法规、细菌命名法规、栽培植物命名法规以及病毒命名法规（草案）。这些法规经过不断地修改,逐渐使生物的命名严谨和完善。在制定这些法规时,拟定者虽参考了其它生物命名的原则、规则和条例,但主要是考虑自身学科内生物的实际情况而定的,因此,上述5个不同的命名法规之间存在着一定的差异,自然会出现一些混乱。为了使国际生物命名的统一化,在国际科协（ICSU）的支持下,1994年国…     

新版国际植物命名法规(维也纳法规)中的主要变化

出版于2006年9月的最新版的《国际植物命名法规》,即维也纳法规（Vienna Code）,取代了圣路易斯法规（Saint Louis Code）而成为管理植物学（包括藻类学和真菌学）科学命名的唯一有效法规。本文报道了维也纳法规和圣路易斯法规之间的主要区别。这些区别包括两版法规在起始日期、有效发表、合格发表、化石植物、多型真菌、拼写和附录诸方面的不同。     

中国农业植物病原菌物常见种属名录

植物病原菌物是造成植物病害的主要病原物,可对生态安全、粮食安全、生物多样性造成重要威胁和灾害.近年来,菌物分类学的研究逐步深入,大量新分类单元被描述、高阶分类系统被修订和完善.在墨尔本和深圳两届国际植物学大会上,对《国际藻类、菌物和植物命名法规》中涉及菌物的部分做出了重大调整以实现"一菌一名".上述研究进展和改变对植物...     

生物学名为什么要用拉丁名称

答:国际植物和动物命名法规的一个基本准则是植物和动物的学名必须是拉丁名称,如果是从其它语言中派生出来的话,至少要给予拉丁化处理。这样就防止了生物命名中出现多种语言命名的混乱局面。拉丁文被选择作为命名的原因主要有二。首先,生物的统一命名始源于林奈的双名法,林奈采用的就是当时欧洲最为通行的语言——拉丁文。其次,拉丁语是死文字,变化甚     

A higher-level taxonomy for hummingbirds

In the context of a recently published phylogenetic estimate for 151 hummingbird species, we provide an expanded informal taxonomy, as well as a formal phylogenetic taxonomy for Trochilidae that follows the precepts of the PhyloCode, but remains consistent with the hierarchical nomenclature of the Linnaean system. We compare the recently published phylogenetic hypothesis with those of prior higher-level and more taxonomically circumscribed phylogenetic studies. We recommend the recognition of nine new clade names under the PhyloCode, eight of which are consistent with tribes and one with a subfamily under the Linnaean system.     

The PhyloCode is fatally flawed, and the “Linnaean” System can easily be fixed

Promoters of the PhyloCode have mounted an intensive and deceptive publicity campaign. At the centerpiece of this campaign have been slogans such as that the Linnaean System will “goof you up,” that the PhyloCode is the “greatest thing since sliced bread,” and that systematists are “afraid” to propose new names because of “downstream consequences.” Aside from such subscientific spin and sloganeering, proponents of the PhyloCode have offered nothing real to back up claims of greater stability for their new system. They have also misled many into believing that the PhyloCode is the only truly phylogenetic system. The confusion that has been fostered involves several discrete arguments, concerning: a new “method” of “designating” names, rank-free taxonomy, uninomial nomenclature, and issues of priority. Claims that the PhyloCode produces a more stable nomenclature are false, as shown with the example of “paleoherbs.” A rank-free system of naming requires an annotated reference tree for even the simplest exchanges of information. This would be confusing at best and would cripple our ability to teach, learn, and use taxonomic names in the field or in publications. We would be confronted by a mass of polynomial names, tied together only by a tree graphic, with no agreed name (except a uninomial, conveying no hierarchy) to use for any particular species. The separate issue of stability in reference to rules of priority and rank can be easily addressed within the current codes, by implementation of some simple changes, as we will propose in this article. Thus there is no need to “scrap” the current Linnaean codes for a poorly reasoned, logically inconsistent, and fatally flawed new code that will only bring chaos.     

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.     

Is the Neotropical flora ready for the PhyloCode?

Nomenclatural systems are structured around classification, and together they enable increasingly informed communication about biological diversity. Challengers of Linnaean classification and nomenclature have proposed the PhyloCode, a new set of rules that would govern the way systematists classify and name the diversity of life. Monographs and floras are two fundamental vehicles for communicating information about plant diversity. These works provide a comprehensive foundation of botanical research upon which other scientific studies are based. Information conveyed by monographs and floras is utilized directly or indirectly both within and outside the scientific arena by a wide range of consumers, such as educators, agronomists, ecologists, conservationists, amateur naturalists, and even lawmakers, to name a few. Both classification and nomenclature are essential to the process of synthesis that leads to monographic and floristic treatments and the communication that they facilitate. Conversion to a new system would have far-reaching consequences for the flow of information from systematics to other scientific disciplines, and to society. The purposes of this article are to address the proposed conversion from the perspective of monographic and floristic research focused on Neotropical plant diversity and to point out some difficulties in applying the PhyloCode to the Neotropical flora. Although we welcome improvements in the current nomenclatural system, we conclude that the PhyloCode is not prepared to replace the Linnaean system as a new way to communicate information about Neotropical plant diversity.     

The PhyloCode: a critical discussion of its theoretical foundation

The definition of taxon names as formalized by the PhyloCode is based on Kripke's thesis of "rigid designation" that applies to Millian proper names. Accepting the thesis of "rigid designation" into systematics in turn is based on the thesis that species, and taxa, are individuals. These largely semantic and metaphysical issues are here contrasted with an epistemological approach to taxonomy. It is shown that the thesis of "rigid designation" if deployed in taxonomy introduces a new essentialism into systematics, which is exactly what the PhyloCode was designed to avoid. Rigidly designating names are not supposed to change their meaning, but if the shifting constitution of a clade is thought to cause a shift of meaning of the taxon name, then the taxon name is not a "rigid designator". Phylogenetic nomenclature either fails to preserve the stability of meaning of taxon names that it propagates, or it is rendered inconsistent with its own philosophical background. The alternative explored here is to conceptualize taxa as natural kinds, and to replace the analytic definition of taxon names by their explanatory definition. Such conceptualization of taxa allows taxon names to better track the results of ongoing empirical research. The semantic as well as epistemic gain is that if taxon names are associated with natural kind terms instead of being proper names, the composition of the taxon will naturally determine the meaning of its name.
© The Willi Hennig Society 2006.     

Towards a new classification of Leguminosae: Naming clades using non-Linnaean phylogenetic nomenclature

The past three decades of research have greatly advanced our understanding of phylogenetic relationships in the family Leguminosae. It has become clear in recent years that our classification system is in need of significant updating if it is to reflect our current understanding of the phylogeny of the family and facilitate effective communication of that knowledge. The goal of this paper is to suggest a set of guidelines for formally defining and naming clades, which draws on many of the recommendations embodied in the draft International Code of Phylogenetic Nomenclature or “PhyloCode”. I provide specific examples of phylogenetic nomenclature applied to several well recognized and well-supported, informally named papilionoid clades to serve as a model for standardizing legume clade names by the legume community in the future. For the most part the clades named here are below subfamily and above tribal ranks in the Linnaean system. It is my contention that a new Linnaean classification, designed to reflect phylogeny, and a clade-based system of phylogenetic nomenclature are mutually complementary approaches to achieving a new classification of the legume family.     

经典植物分类学的发展与iFlora

简要介绍了经典植物分类的基础工作,即鉴定、描述、命名和分类,以及发展动向。作者认为计算机辅助鉴定（如delta intkey）将成为形态鉴定的常规手段;模式识别技术是植物图像鉴定的发展方向;突出物种遗传本质的分子鉴定将成为植物物种鉴定的核心。DELTA系统或类似的符合计算机逻辑的分类学描述语言将成为新一代植物志（iFlora）的基本语言。近20年来,一些学者逐渐表现出对现行植物命名法规的质疑和修改意愿,特别是生物法规草案（Draft BioCode）和谱系法规（PhyloCode）两个试行法规的诞生。它们促进对法规的革新与完善,并在iFlora中得以体现。以APG系统为代表的分子系统发育研究已经成为植物系统分类研究的主流,但在物种层面,物种的界定仅仅依靠分子信息显然是不够的,而必须运用综合的特征性状信息进行分析解读,真正实现物种在形态、遗传信息等综合性状的融合统一。了解和掌握这些新的技术和研究成果,无疑对于iFlora设计和编研有着重要的参考意义,而基于新技术和新理念的iFlora也将成为植物分类最新发展成果的集中体现。     

Paraphyletic group,PhyloCode and phylogenetic species—the current debate and a preliminary commentary

In this essay, three currently hotly debated issues in biological systematics, i.e., the paraphyletic group, the PhyloCode, and the phylogenetic species concept, have been briefly reviewed. (1) It is widely acknowledged that cladistics has made some positive contributions to the study of systematics. In particular, the employment of outgroup analysis for assessing character polarities, the application of synapomorphies to the inference of relationships between taxa, and the use of cladistic methods for reconstructing phylogeny, have all greatly facilitated the improvement of systematic approaches. A fatal flaw in cladistics is its refusal to accept paraphyletic groups. Frankly, we are adherents and practitioners of phyletics, and hence consider paraphyletic groups to be acceptable. For example, an AFLP analysis has shown that Zabelia (Caprifoliaceae) can be included in Abelia, but the members in Zabelia differ from those in Abelia not only in pollen morphology, but also in having persistent petioles dilated and connate at base, thus enclosing axillary buds, characters of adaptive significance obtained possibly when Zabelia members entered a new ecological niche, so we consider that they are better treated as two independent genera, though indeed such a treatment makes Abelia paraphyletic. (2) Some cladists pointed out that as the tool for communication and the system for information storage and retrieval, biological nomenclature is required to be unambiguous, unique and stable. They criticise the Linnaean rank-based system of nomenclature for failing to satisfy such requirements for the naming of clades and species. To address this problem, the PhyloCode is proposed in recent years, in which three definitions for clade naming are given, i.e., the node-based, the stem-based, and the apomorphy-based. We are of the opinion that since the Linnaean binominal system of botanical nomenclature has existed for nearly 250 years, the rejection of this system and the adoption of the PhyloCode would create a state of chaos in botanical nomenclature. This does not mean that there exist no merits in the proposals made by the PhyloCode supporters. We suggest that further studies should be conducted for its practical application. (3) It has been well known that there are many problems with the application of the biological species concept in plants, and thus at the present time the majority of plant systematists actually seldom use this concept in their practical work. The rapid development of cladistic approach has motivated the proposal of the phylogenetic species concept. This species concept is established based on three criteria, i.e., the autamorphy, the diagnosability and the basal exclusivity, hence the autamorphy species concept, the diagnosability species concept, and the genealogical concept are created respectively. Nevertheless, the morpho-geographical species concept is still predominantly adopted in plant systematics. When using this species concept, however, we should also take into account the data from other sources, particularly those from pollination biology, breeding system and molecular systematics.     

Phylogeny,classification and nomenclature: a reply to F. Pleijel and G. W. Rouse

In systematics, the uncovering of monophyletic units, of sister group relationships and also of paraphyla is an important part of primary research. The hypotheses derived are thus subject to falsification and are subject to change. In contrast, classifications are a secondary step, as they are derived from such hypotheses. Classifications are based on different philosophies, which permit different solutions as to how results in the fields of taxonomy and phylogenetics can be transposed into a ‘system’. The function of classifications is at least partly utilitarian, and this is even more true for the names and principles of nomenclature. Nomenclature is simply a tool for information retrieval and for safeguarding understanding. Directly linking names and cladograms or nodes, respectively – making them subject to changes by falsification – would deliberately ignore the primary, strictly utilitarian function of long‐established principles of nomenclature and would endanger an instrument that functions almost perfectly. Approaches to introduce a so‐called PhyloCode should therefore not be pursued, as there is no chance at all that this kind of code could be generally accepted.