A common registration-to-publication automated pipeline for nomenclatural acts for higher plants (International Plant Names Index,IPNI), fungi (Index Fungorum,MycoBank) and animals (ZooBank)

Collaborative effort among four lead indexes of taxon names and nomenclatural acts ( International Plant Name Index (IPNI), Index Fungorum, MycoBank and ZooBank) and the journals PhytoKeys, MycoKeys and ZooKeys to create an automated, pre-publication, registration workflow, based on a server-to-server, XML request/response model. The registration model for ZooBank uses the TaxPub schema, which is an extension to the Journal Tag Publishing Suite (JATS) of the National Library of Medicine (NLM). The indexing or registration model of IPNI and Index Fungorum will use the Taxonomic Concept Transfer Schema (TCS) as a basic standard for the workflow. Other journals and publishers who intend to implement automated, pre-publication, registration of taxon names and nomenclatural acts can also use the open sample XML formats and links to schemas and relevant information published in the paper.     

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.     

Definitions in phylogenetic taxonomy: critique and rationale

A general rationale for the formulation and placement of taxonomic definitions in phylogenetic taxonomy is proposed, and commonly used terms such as "crown taxon" or "node-based definition" are more precisely defined. In the formulation of phylogenetic definitions, nested reference taxa stabilize taxonomic content. A definitional configuration termed a node-stem triplet also stabilizes the relationship between the trio of taxa at a branchpoint, in the face of local change in phylogenetic relationships or addition/deletion of taxa. Crown-total taxonomies use survivorship as a criterion for placement of node-stem triplets within a taxonomic hierarchy. Diversity, morphology, and tradition also constitute heuristic criteria for placement of node-stem triplets.     

Taxon mapping exemplifies punctuated equilibrium and atavistic saltation

Two or more exemplars of the same taxon forming a nonmonophyletic group on a molecular tree may be viewed as representing surviving populations of a deep shared ancestral taxon, and if different species of the same genus, then theoretically phenotypically static remnants of punctuated equilibrium. That taxon may be mapped on a molecular cladogram and evolutionarily resolved at the taxon level inclusive of all exemplars. The technique for mapping taxa on a molecular tree, termed here caulistics, is much like mapping traits but recovers macroevolutionary information at the taxon level. All lineages arising from the mapped taxon are its direct descendants. Mapped taxa superimposed or overlapping may reveal packaged adaptive traits. When a mapped taxon is well split by another mapped taxon on a molecular tree, atavistic saltation based on triggering an epigenetically retained trait complex is a theoretical explanation. Caulistics combines traditional taxonomy and molecular phylogenetics to reveal previously unknown aspects of the macroevolutionary past.     

A cryptic taxon of Galápagos tortoise in conservation peril

As once boldly stated, 'bad taxonomy can kill', highlighting the critical importance of accurate taxonomy for the conservation of endangered taxa. The concept continues to evolve almost 15 years later largely because most legal protections aimed at preserving biological diversity are based on formal taxonomic designations. In this paper we report unrecognized genetic divisions within the giant tortoises of the Galápagos. We found three distinct lineages among populations formerly considered a single taxon on the most populous and accessible island of Santa Cruz; their diagnosability, degree of genetic divergence and phylogenetic placement merit the recognition of at least one new taxon. These results demonstrate the fundamental importance of continuing taxonomic investigations to recognize biological diversity and designate units of conservation, even within long-studied organisms such as Galápagos tortoises, whose evolutionary heritage and contribution to human intellectual history warrant them special attention.     

Least-inclusive taxonomic unit: a new taxonomic concept for biology

Phylogenetic taxonomy has been introduced as a replacement for the Linnaean system. It differs from traditional nomenclature in defining taxon names with reference to phylogenetic trees and in not employing ranks for supraspecific taxa. However, 'species' are currently kept distinct. Within a system of phylogenetic taxonomy we believe that taxon names should refer to monophyletic groups only and that species should not be recognized as taxa. To distinguish the smallest identified taxa, we here introduce the least-inclusive taxonomic unit (LITU), which are differentiated from more inclusive taxa by initial lower-case letters. LITUs imply nothing absolute about inclusiveness, only that subdivisions are not presently recognized.     

Nomenclatural benchmarking: the roles of digital typification and telemicroscopy

Nomenclatural benchmarking is the periodic realignment of species names with species theories and is necessary for the accurate and uniform use of Linnaean binominals in the face of changing species limits. Gaining access to types, often for little more than a cursory examination by an expert, is a major bottleneck in the advance and availability of biodiversity informatics. For the nearly two million described species it has been estimated that five to six million name-bearing type specimens exist, including those for synonymized binominals. Recognizing that examination of types in person will remain necessary in special cases, we propose a four-part strategy for opening access to types that relies heavily on digitization and that would eliminate much of the bottleneck: (1) modify codes of nomenclature to create registries of nomenclatural acts, such as the proposed ZooBank, that include a requirement for digital representations (e-types) for all newly described species to avoid adding to backlog; (2) an "r" strategy that would engineer and deploy a network of automated instruments capable of rapidly creating 3-D images of type specimens not requiring participation of taxon experts; (3) a "K" strategy using remotely operable microscopes to engage taxon experts in targeting and annotating informative characters of types to supplement and extend information content of rapidly acquired e-types, a process that can be done on an as-needed basis as in the normal course of revisionary taxonomy; and (4) creation of a global e-type archive associated with the commissions on nomenclature and species registries providing one-stop-shopping for e-types. We describe a first generation implementation of the "K" strategy that adapts current technology to create a network of Remotely Operable Benchmarkers Of Types (ROBOT) specifically engineered to handle the largest backlog of types, pinned insect specimens. The three initial instruments will be in the Smithsonian Institution(Washington, DC), Natural History Museum (London), and Museum National d'Histoire Naturelle (Paris), networking the three largest insect collections in the world with entomologists worldwide. These three instruments make possible remote examination, manipulation, and photography of types for more than 600,000 species. This is a cybertaxonomy demonstration project that we anticipate will lead to similar instruments for a wide range of museum specimens and objects as well as revolutionary changes in collaborative taxonomy and formal and public taxonomic education.     

歧隐翅虫亚族(鞘翅目,隐翅虫科)分类特征分析及单系性质疑

一个分类阶元是否单系,在当代分类学与系统学的意义上直接决定这个分类阶元的有效性,即可否广泛接受.形态学分析和动物地理分布模式可以提供非常有价值的启示.鞘翅目隐翅虫科隐翅虫亚科隐翅虫族的歧隐翅虫亚族Anisolinina Hayashi,1993(Coleoptera,Staphylinidae,Staphylininae),尽管是一个建立不久的分类单元,但亚族的分类定义、包括的种属、以及各属种的相互关系等,最近发生了较大的变化.通过分析一些重要的、用来定义这个亚族的关键形态性状,如前胸背板缘折上缘线与下缘线、上颚须、下唇须等,比较亚族内各属级单元的分类历史与动物地理分布,揭示歧隐翅虫亚族Anisolinina不是一个单系类群.     

A numerical taxonomic study of Cucurbita

Several statistical techniques of numerical taxonomy were studied by using 21 species ofCucurbita as models. Data were taken on 93 plant characters for 24 operational taxonomic units (OTU’s). Three similarity coefficients, Q-correlation, distance and divergence, were used to compute phenetic similarities among the 24 OTU’s. The results are summarized in the form of eight phenograms using both unweighted and weighted pair-group methods of clustering. The results obtained from the various statistical techniques were compared with cross-compatibility ratings. The distance and divergence coefficients and their respective phenogram values were more highly correlated with the cross-compatibility ratings than were the Qcorrelation coefficients and their phenogram values. However, from a subjective viewpoint, the phenograms derived from Q-correlation coefficients were in closer general agreement with a combination of biological factors including cross compatibility, geographical distribution, and ecological adaption than were phenograms derived from distance or divergence coefficients.     

淫羊藿属植物的数量分类学研究

通过观测淫羊藿属植物的30个质量性状和15个数量性状,利用聚类分析和主成分分析的方法研究淫羊藿属属下类群的分类关系。结果表明:(1)聚类分析结果将淫羊藿属中国种类划分为大花类群和小花类群,支持Stearn对Sect.Macroceras、Sect.Polyphyllon和Subg.Rhizophyllum的处理,但认为Sect.Epimedium的分类地位尚需进一步探讨。(2)主成分分析结果显示,性状的累积贡献率不是很高,前3个主成分累积贡献率为51.86%,这可能与本属植物演化过程中性状变异的多样化和复杂化相关,但由主成分分析的结果仍可以看出中国种类被划分为大花类群和小花类群。研究认为,花瓣与内萼片长度比、花瓣是否具距、萼片轮数等作为主成分反映的性状对淫羊藿属分类具有重要价值。     

The fungi kingdom: heterogeneity of physiological-biochemical properties and closeness to plants, animals, and prokaryotes

This review analyzes the current taxonomy of fungi whose criteria are based on a range of episemantic molecules. In this context, data on the chemical composition of fungal cells (membrane lipids, cytosolic carbohydrates, etc.) are considered in comparison with their counterparts found in higher eukaryotes and prokaryotes. Modern theories explaining the origin of fungi and their similarity to plants, animals, and bacteria are discussed. The biochemical criteria used in this work supported the division of fungi into Eumycota and Neomycota. The latter division, especially Basidiomycota, are more closely related to plants. The heterogeneity of the kingdom Fungi is underlined, the existence of Oomycota as a separate entity is supported, and the theory of the primitive nature of fungal cells is criticized from the viewpoint of biochemical adaptation.     

20种山茶科植物的叶表皮微形态研究

为解决一些山茶科(Theaceae)的分类学问题,该研究在光学显微镜下对山茶科2亚科6属共20种植物的13种叶表皮微形态特征进行了观察,并利用聚类分析和主成分分析对这些特征进行分析,为山茶科的科学分类提供参考资料。结果表明:(1)山茶科20种植物的13种叶表皮微形态特征能够区分种间差异和分类等级,显示了比较全面的分类价值。(2)基于微形态特征的聚类分析和主成分分析结果显示,20个种分为2个大类群以及10个分支,很好地区分了山茶亚科(Theoideae)与厚皮香亚科(Ternstroemoideae),并将大部分分类地位相近的物种归类到一起,较好地反映了物种之间的亲缘关系。(3)该研究结果支持将小黄花茶组(Sect.Luteoflora)作为独立的一个组;支持将重庆山茶(Camellia chungkingensis Chang)从瘤果茶组(Sect.Tuberculata Chang Tax.)中分离;支持将山茶亚科与厚皮香亚科划分为两个较大类群,认为将厚皮香亚科并入五列木科(Pentaphylacaceae)的观点还有待更多实验证据的支持。     

The Kingdom Fungi: Heterogeneity of Physiological and Biochemical Properties and Relationships with Plants,Animals, and Prokaryotes (Review)

This review analyzes the current taxonomy of fungi whose criteria are based on a range of episemantic molecules. In this context, data on the chemical composition of fungal cells (membrane lipids, cytosolic carbohydrates, etc.) are considered in comparison with their counterparts found in higher eukaryotes and prokaryotes. Modern theories explaining the origin of fungi and their similarity to plants, animals, and bacteria are discussed. The biochemical criteria used in this work supported the division of fungi into Eomycota and Neomycota. The latter division, especially Basidiomycota, are more closely related to plants. The heterogeneity of the Fungi kingdom is emphasized, the existence of Oomycota as a separate entity is supported, and the theory of the primitive nature of fungal cells is criticized from the viewpoint of biochemical adaptation.     

Molecular Taxonomy of Phytopathogenic Fungi: A Case Study in Peronospora

Background

Inappropriate taxon definitions may have severe consequences in many areas. For instance, biologically sensible species delimitation of plant pathogens is crucial for measures such as plant protection or biological control and for comparative studies involving model organisms. However, delimiting species is challenging in the case of organisms for which often only molecular data are available, such as prokaryotes, fungi, and many unicellular eukaryotes. Even in the case of organisms with well-established morphological characteristics, molecular taxonomy is often necessary to emend current taxonomic concepts and to analyze DNA sequences directly sampled from the environment. Typically, for this purpose clustering approaches to delineate molecular operational taxonomic units have been applied using arbitrary choices regarding the distance threshold values, and the clustering algorithms.

Methodology

Here, we report on a clustering optimization method to establish a molecular taxonomy of Peronospora based on ITS nrDNA sequences. Peronospora is the largest genus within the downy mildews, which are obligate parasites of higher plants, and includes various economically important pathogens. The method determines the distance function and clustering setting that result in an optimal agreement with selected reference data. Optimization was based on both taxonomy-based and host-based reference information, yielding the same outcome. Resampling and permutation methods indicate that the method is robust regarding taxon sampling and errors in the reference data. Tests with newly obtained ITS sequences demonstrate the use of the re-classified dataset in molecular identification of downy mildews.

Conclusions

A corrected taxonomy is provided for all Peronospora ITS sequences contained in public databases. Clustering optimization appears to be broadly applicable in automated, sequence-based taxonomy. The method connects traditional and modern taxonomic disciplines by specifically addressing the issue of how to optimally account for both traditional species concepts and genetic divergence.     

Reassessing evolutionary relationships of scleractinian corals

The widely accepted family tree of Scleractinia published by Wells, based on a combination of morphological coral taxonomy and the fossil record, has recently been revised by Veron. It is now possible to test the validity of some of the conclusions reached by these and other authors by the use of molecular techniques. This paper reviews the results to date. Studies of ribosomal DNA have shown that the Scleractinia are monophyletic, i.e. derived from the same ancestral taxon. Extensions of this same data set now indicate that the Poritidae and Dendrophylliidae, with their fossil antecedents, may each warrant separate suborder status. They further suggest (a) that the Suborder Faviina (faviids, mussids and their allies) should probably be retained as a monophyletic group and (b) that Wells' original account of the isolated position of the Pocilloporidae and Astrocoeniidae is correct. These conclusions all accord with Veron's family tree. However, the Fungiina, even after removal of the Poritidae, are unlikely to be a monophyletic group at suborder level. The molecular data further show that externally observable morphological characters used in the taxonomy of extant corals distinguish families more reliably than do internal micro-skeletal characters frequently used in coral palaeontology.