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.     

Selected subspecies names from Richter,Plantae Europeae,Vol. 1, 1890

The bookK. Richter, Plantae europeae, Vol. 1, 1890, is analyzed from the viewpoint of nomenclature of subspecies names. 264 subspecies names interesting from the standpoint of contemporary taxonomy and nomenclature are selected from the total number of 840 subspecies names for a commented list. Seventeen important cases are dealt with separately in greater detail. Eleven new nomenclatural combinations (two for species, nine for subspecies) are proposed in the Appendix. Types for two generic names (Acorellus Palla andJuncellus C. B. Clarke) are proposed. A new term “parabasionym” is applied for names establishing the priority of infraspecific epithets in the rank in question. The need to respect the newly accepted principle of priority of autonymic subspecies names at proposing new nomenclatural combinations is stressed. Examples ofRichter’s subspecies names having priority, subspecies names with necessary changes in their authorship and names having a possible importance as parabasionyms are enumerated in separate lists.     

A Perspective on Protistan Nomenclature

ABSTRACT. The nomenclature of protists is more complicated than that of plants or animals because more than one code of nomenclature applies (i.e. the taxa may be ambiregnal), because of the frequent absence of type material, and because of changing perspectives of the phylogenetic relationships of various groups of protists. These factors often lead to uncertainty over the meaning of names of taxa. If nomenclatural instability is to be avoided, some changes in current practices are required. The nature of the problems and some possible changes are discussed.     

Zoological nomenclature in the digital era

Creation and use of the scientific names of animals are ruled by the International Code of Zoological Nomenclature. Until recently, publication of new names in a work produced with ink on paper was required for their availability. A long awaited amendment to the Code issued in September 2012 by the International Commission on Zoological Nomenclature now allows publication of new names in online-only works, provided that the latter are registered with ZooBank, the Official Register of Animal Names. With this amendment, the rules of zoological nomenclature have been aligned with the opportunities (and needs) of our digital era. However, possible causes for nomenclatural instability remain. These could be completely removed if the Code-compliant publication of new names will be identified with their online registration, under suitable technological and formal (legal) conditions. Future developments of the ZooBank may provide the tool required to make this definitive leap ahead in zoological nomenclature.     

The importance of designating type material for uncultured taxa

Naming of uncultured Bacteria and Archaea is often inconsistent with the International Code of Nomenclature of Prokaryotes. The recent practice of proposing names for higher taxa without designation of lower ranks and nomenclature types is one of the most important inconsistencies that needs to be addressed to avoid nomenclatural instability. The Code requires names of higher taxa up to the rank of class to be derived from the type genus name, with a proposal pending to formalise this requirement for the rank of phylum. Designation of nomenclature types is crucial for providing priority to names and ensures their uniqueness and stability. However, only legitimate names proposed for axenic cultures can be used for this purpose. Candidatus names reserved for taxa lacking cultured representatives may be granted this right if recent proposals to use genome sequences as type material are endorsed, thereby allowing the Code to be fully applied to lineages represented by metagenome-assembled genomes (MAGs) or single amplified genomes (SAGs). Genome quality standards need to be considered to ensure unambiguous assignment of type material. Here, we illustrate the recommended practice by proposing nomenclature type material for four major uncultured prokaryotic lineages based on high-quality MAGs in accordance with the Code.     

Index nominum familiarum plantarum vascularium

A list of 2510 vascular plant family names is provided, valid and not validly published as well as legitimate and not legitimate. Each entry has a full bibliographic reference, nomenclatural status, generic type (when based on a generic name), means of validation, original place of publication for pre-1789 works, isonyms, invalid names proposed prior to a name’s validation, first use of correct orthography (if not given in the original publication), first uses of other orthographic variations, divisional placements of typified names, indication of acceptance in the botanical literature after 1960, and a four-letter abbreviation for the legitimate family name. In addition, nomenclaturally correct, typified names are listed for the ranks of order, superorder, subclass, class, subdivision, division/phylum, and subkingdom (for a total of 753 names), with full bibliographic citations. A similar list of 1569 currently available extant vascular plant family names is also given, of which 960 are considered to be in “current use.” A starting date for all names is assumed to be 4 August 1789 (Jussieu,Generaplantarum). Current difficulties with family nomenclature, and potential changes to bibliographic citations as a result of recently proposed changes to theInternational Code of Botanical Nomenclature, are noted.     

Invalidly published names inJanchen's “Catalogus florae Austriae”: Survey,analysis, and notes

Names of species and subspecies fromJanchen's Catalogus were revised with regard to their validity; invalidly published names were compiled in a commented list of 120 names. About sixty of them were analyzed at length from nomenclatural and taxonomical viewpoints. The cause of the invalidity of these names were discussed; omission of citations of basionyms to proposals of new nomenclatural combinations is the main reason for the invalidity ofJanchen's names. Taxonomic reclassifications and nomenclatural revisions resulted in 23 new nomenclatural combinations, five of these proposals representing direct validations ofJanchen's invalidly published names. Some more general problems of nomenclature are discussed: indirect validation of invalidly published names; omission of infraspecific homonymy; the correctness and necessity to attach neglected authors' names to the names of plants based on those names distinctly taken over from such authors; problems of autonyms in the ICBN Code. The use of the category “convarietas” in cultivated plants (instead of subspecies) is emphasized. Names validated byJanchen himself in his paper of 1959 should be used with this publication place instead of their invalid publication in the Catalogus. Some propositions for future research by other authors are also added.     

Taxonomic indexing--extending the role of taxonomy

Taxonomic indexing refers to a new array of taxonomically intelligent network services that use nomenclatural principles and elements of expert taxonomic knowledge to manage information about organisms. Taxonomic indexing was introduced to help manage the increasing amounts of digital information about biology. It has been designed to form a near basal layer in a layered cyberinfrastructure that deals with biological information. Taxonomic Indexing accommodates the special problems of using names of organisms to index biological material. It links alternative names for the same entity (reconciliation), and distinguishes between uses of the same name for different entities (disambiguation), and names are placed within an indefinite number of hierarchical schemes. In order to access all information on all organisms, Taxonomic indexing must be able to call on a registry of all names in all forms for all organisms. NameBank has been developed to meet that need. Taxonomic indexing is an area of informatics that overlaps with taxonomy, is dependent on the expert input of taxonomists, and reveals the relevance of the discipline to a wide audience.     

Prokaryotic taxonomy and nomenclature in the age of big sequence data

The classification of life forms into a hierarchical system (taxonomy) and the application of names to this hierarchy (nomenclature) is at a turning point in microbiology. The unprecedented availability of genome sequences means that a taxonomy can be built upon a comprehensive evolutionary framework, a longstanding goal of taxonomists. However, there is resistance to adopting a single framework to preserve taxonomic freedom, and ever increasing numbers of genomes derived from uncultured prokaryotes threaten to overwhelm current nomenclatural practices, which are based on characterised isolates. The challenge ahead then is to reach a consensus on the taxonomic framework and to adapt and scale the existing nomenclatural code, or create a new code, to systematically incorporate uncultured taxa into the chosen framework.Subject terms: Archaea, Bacteria     

Constraints in naming parts of the Tree of Life

There are now overlapping codes of nomenclature that govern some of the same names of biological taxa. The International Code of Zoological Nomenclature (ICZN) uses the non-evolutionary concept of a "type species" to fix the names of animal taxa to particular ranks in the nomenclatural hierarchy. The PhyloCode, in contrast, uses phylogenetic definitions for supraspecific taxa at any hierarchical level within the Tree of Life (without associating the names to particular ranks), but does not deal with the names of species. Thus, biologists who develop classifications of animals need to use both systems of nomenclature, or else operate without formal rules for the names of some taxa (either species or many monophyletic groups). In addition, the ICZN does not permit the unique naming of many taxa that are considered to be between the ranks of genus and species. Hillis and Wilcox [Hillis, D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Mol. Phylogenet. Evol. 34, 299-314] provided recommendations for the classification of New World true frogs that utilized the ICZN to provide names for species, and the PhyloCode to provide names for supraspecific taxa. Nonetheless, they created new taxon names that followed both sets of rules, to avoid conflicting classifications. They also recommended that established names for both species and clades be used whenever possible, to stabilize the names of both species and clades under either set of rules, and to avoid conflicting nomenclatures. Dubois [Dubois, A., 2006. Naming taxa from cladograms: a cautionary tale. Mol. Phylogenet. Evol., 42, 317-330] objected to these principles, and argued that the names provided by Hillis and Wilcox [Hillis, D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Mol. Phylogenet. Evol. 34, 299-314] are unavailable under the ICZN, and that the two nomenclatural systems are incompatible. Here, I argue that he is incorrect in these assertions, and present arguments for retaining the established names of New World true frogs, which are largely compatible under both sets of nomenclatural rules.     

Nomencurator: a nomenclatural history model to handle multiple taxonomic views

Evolutionary studies are generating increasing numbers of phylogenies which, in turn, sometimes result in changes to hierarchical organization and therefore changes in taxonomic nomenclature. A three-layered data model for a nomenclature database has been developed in order to elucidate the information structure in nomenclature and as a means to organize and manage a large, dynamic knowledge-base. In contrast to most other taxonomic databases, the model is publication-oriented rather than taxon-oriented and dynamic rather than static, in order to mimic the processes that taxonomists use naturally. The three-layered structure requires data integrity localized to each publication, instead of global data integrity, which relaxes constraints common to taxonomic databases and permits multiple taxonomic opinions: taxon names are made available as metadata within the model. Its prototype implementation, written in C ⁺⁺, has an autonomous self-identification mechanism to avoid spurious data-inflation in a publication-oriented data model. Self-identification is also desirable for distributed implementations of the nomenclature database. Publication-oriented design also will make maintenance easier than for taxon-oriented databases, much of the maintenance workload being amenable to automation. The three-layered data model was designed for use by taxonomists, but is also able to provide concise, reduced expression for non-experts required in biodiversity research, for example.     

Nomenclatural rules in zoology as a potential threat against natural history museums

Natural history museums store millions of organisms from the whole world that are of great use to understand the evolution, structure and problems of biodiversity. One of their main functions is to act as repositories of so-called type specimens or onomatophores. These allow long-term universality and stability of biological nomenclature through providing an objective and permanent link between the world of language and the world of organisms. Threats currently exist against this function, in two directions at least. (1) Recent changes to the nomenclatural rules put the emphasis on ‘usage’ of nomina and challenge ‘priority’ as the basic principle of nomenclature. This entails a shift from specimens to concepts or tradition for the establishment of the valid nomina of taxa. Beside its encouraging taxonomists to work carelessly and hastily, this attitude weakens the significance and importance of those specimens in taxonomy, undermining their important flag function for the image, funding and even the mere existence of natural history museums. To counter this tendency, any validation of junior synonyms or homonyms to protect usage should be strictly limited to nomina in well-documented very widespread use, not only in specialized systematic publications but in the general scientific and non-scientific literature and in society as a whole. (2) For the same reason, nomenclatural systems that rely not on onomatophores but on verbal definitions of nomina should not be encouraged. It is crucial that the unique value of onomatophores be highlighted, and that the institutions which care for their long-term conservation and scientific managing be recognised and permanently provided with appropriate funding and staff. Many other disciplines of biology do or will benefit from such a support to museums.     

T. R. R. Stebbing:A bibliography with biographic notes

T. R. R. Stebbing (1835–1926), a specialist on the systematics of amphipod Crustacea, was raised in London in a literary family and studied classics, law and history at Oxford. After his ordination as a priest in 1859 he was a schoolmaster, then, after he married, a private tutor at Torquay. About 1863 he read Darwin's Origin of species and was convinced by it; by 1868 he had become a naturalist and systematist. In 1877 he moved to Tunbridge Wells where he spent the rest of his life studying Crustacea, active in scientific societies, and writing essays and reviews.
Stebbing's Darwinism was not particularly original, though he marshalled some good examples from the invertebrates to indicate the importance of variation within and between species. He regarded natural selection as a directing force by which God's plan for organisms was being worked out, and credited it with the origin of language, morality and religion. In taxonomic practice, Stebbing advocated priority of names, simple rules of transliteration and gender, and publication of new names only in a few easily-accessible journals. After the publication of the Regies internationales de la nomenclature zoologique in 1905 his writings on taxonomic practice were confined to minor issues.
A bibliography of Stebbing's 242 publications concerned with carcinology, Darwinism, nomenclature and miscellaneous subjects has been compiled.     

AVIAN NOMENCLATURAL ISSUES ARISING FROM THE PUBLICATION OF ROOKMAAKER'S THE ZOOLOGICAL EXPLORATION OF SOUTHERN AFRICA 1650–1790

Clancey, P. A. & Brooke, R. K. 1990. Avian nomenclatural issues arising from the publication of Rook-maaker's The Zoological Exploration of Southern Africa 1650–1790. Ostrich 61:143-145.

Rookmaaker (1989) has drawn the attention of taxonomists to the existence of a range of long overlooked senior ornithological synonyms which, if adopted in terms of the Law of Priority, would result in changes to long established names. As such extensive changes of name are patently undesirable, we propose a course of action which would entail as little disruption as possible to current usage, and obviate the necessity for the submission of cases to the International Commission on Zoological Nomenclature.     

Naming taxa from cladograms: a cautionary tale

The recent publication of a new hypothesis of cladistic relationships among American frogs referred to the genus Rana, accompanied by a new taxonomy and a new nomenclature of this group [Hillis D.M., Wilcox, T.P., 2005. Phylogeny of the New World true frogs (Rana). Molecular Phylogenetics and Evolution 34, 299-314], draws attention to the problems posed by the use of a "double nomenclature", following both the rules of the International Code of Zoological Nomenclature (designated here as "onomatophore-based nomenclature") and the rules of the draft Phylocode (designated here as "definition-based nomenclature"). These two nomenclatural systems, which rely upon widely different theoretical bases, are incompatible, and the latter cannot be viewed as a "modification" of the former. Accordingly, scientific names (nomina) following both systems should be clearly distinguished in scientific publications. Onomatophore-based nomina should continue to be written as they have been for about 250 years, whereas definition-based nomina should be written in a specific way, e.g., Lithobates. The combined use of both nomenclatural systems for the same taxonomy in the same paper requires good knowledge and careful respect of the rules of the Code regarding availability, allocation and validity of nomina. As shown by this example, not doing so may result in various problems, in particular in publishing nomina nuda or in using nomenclatural ranks invalid under the current Code. Attention is drawn to the fact that new nomina published without diagnostic characters are not available under the Code, and that the latter currently forbids the use of more than two ranks (subgenus and "aggregate of species") between the ranks genus and species.     

The Linnaean system and its 250-year persistence

The Linnaean system of nomenclature has been used and adapted by biologists over a period of almost 250 years. Under the current system of codes, it is now applied to more than 2 million species of organisms. Inherent in the Linnaean system is the indication of hierarchical relationships. The Linnaean system has been justified primarily on the basis of stability. Stability can be assessed on at least two grounds: the absolute stability of names, irrespective of taxonomic concept; and the stability of names under changing concepts. Recent arguments have invoked conformity to phylogenetic methods as the primary basis for choice of nomenclatural systems, but even here stability of names as they relate to monophyletic groups is stated as the ultimate objective. The idea of absolute stability as the primary justification for nomenclatural methods was wrong from the start. The reasons are several. First, taxa are concepts, no matter the frequency of assertions to the contrary; as such, they are subject to change at all levels and always will be, with the consequence that to some degree the names we use to refer to them will also be subject to change. Second, even if the true nature of all taxa could be agreed upon, the goal would require that we discover them all and correctly recognize them for what they are. Much of biology is far from that goal at the species level and even further for supraspecific taxa. Nomenclature serves as a tool for biology. Absolute stability of taxonomic concepts—and nomenclature—would hinder scientific progress rather than promote it. It can been demonstrated that the scientific goals of systematists are far from achieved. Thus, the goal of absolute nomenclatural stability is illusory and misguided. The primary strength of the Linnaean system is its ability to portray hierarchical relationships; stability is secondary. No single system of nomenclature can ever possess all desirable attributes: i.e., convey information on hierarchical relationships, provide absolute stability in the names portraying those relationships, and provide simplicity and continuity in communicating the identities of the taxa and their relationships. Aside from myriad practical problems involved in its implementation, it must be concluded that “phylogenetic nomenclature” would not provide a more stable and effective system for communicating information on biological classifications than does the Linnaean system.     

《中国真菌志》50年编研成果及展望

历经几代真菌人的艰苦奋斗,《中国真菌志》目前已出版65卷,其中子囊菌类有35卷、担子菌类26卷、接合菌类1卷、卵菌1卷、黏菌2卷;上述卷册记录923属9 228种及种下分类群。编研涉及大型和小型的类群、腐生菌、食药用菌、菌根真菌、作物和林木病原菌、捕食性真菌、虫生菌、菌生真菌以及毒菌等。编研过程中发现并发表了大量新分类群,丰富了对菌物物种多样性的认知。归纳已有成果,已立项卷册应加快编研和出版进度;资源调查与分类学研究需进一步加强,按分类群(专科、专属)继续开展编研工作,注重拟参编类群的前期研究积累;以下分类群值得在后续工作中予以关注：水霉目等部分卵菌、壶菌类、座囊菌纲部分类群、盘菌纲和锤舌菌纲中尚未参编的主要类群、伞菌纲中具有小型子实体的类群等。由于分类系统在不断更新和完善,已出版卷册中使用的部分名称和分类地位的处理需依据被大多数学者所公认的分类系统给予适时的订正。期待建设一支继往开来的菌物分类学研究队伍,不断取得令世人瞩目的编研成果,为我国菌物资源利用和物种保护提供科学依据。     

Forum – Taxonomic Stability is Ignorance

Absolute nomenclatural stability is undesirable in phylogenetic classifications because they reflect changing hypotheses of cladistic relationships. De Queiroz and Gauthier's (1990: Syst. Zool. 39, 307–322; 1992: A. Rev. Ecol. Syst. 23, 449–480; 1994: Trends Ecol. Evol. 9, 27–31) alternative to Linnaean nomenclature is concluded to provide stable names for unstable concepts. In terms of communicating either characters shared by species of a named taxon or elements (species) included in a taxon, de Queiroz and Gauthier's system is less stable than the Linnaean system. Linnaean ranks communicate limited information about inclusivity of taxa, but abandonment of ranks results in the loss of such information. As cladistic hypotheses advance, taxa named under de Queiroz and Gauthier's system can change their level of generality radically, from being part of a group to including it, without any indicative change in its spelling. The Linnaean system has been retained by taxonomists because its hierarchic ranks are logically compatible with nested sets of species, monophyletic groups, and characters. Other authors have offered conventions to increase the cladistic information content of Linnaean names or to replace them with names that convey cladistic knowledge in greater detail; de Queiroz and Gauthier sacrifice the meaning of taxon names and categorical ranks in favor of spelling stability.