Third meeting of the International Society for Phylogenetic Nomenclature: a report

The Third Meeting of the International Society for Phylogenetic Nomenclature (ISPN) convened at Dalhousie University in Halifax, Canada, from 20 to 22 July 2008. In addition to contributed talks, the conference included a progress report on the PhyloCode 'Companion Volume', a discussion of how to complete this book in a timely fashion, a demonstration of the online registration data base (RegNum), plenary talks, and Council and business meetings. Topics discussed at the meeting include problems created by rank-based nomenclature in various eukaryotic taxa, dealing with hybrids in rank-based and phylogenetic nomenclature, phyloinformatics, the choice of names to use when the taxonomic content associated with available names varies, teaching phylogenetic nomenclature, and the application of phylogenetic nomenclature to specific taxa.     

First International Phylogenetic Nomenclature Meeting: a report

The First International Phylogenetic Nomenclature Meeting convened in Paris from July 6–9, 2004 in the Muséum National d'Histoire Naturelle. This meeting marked a turning point in the history of biological nomenclature — the inauguration of a new society (the International Society for Phylogenetic Nomenclature) that will soon launch a code of phylogenetic nomenclature (the PhyloCode) that will represent a fundamental change in the way in which taxon names are defined.     

The PhyloCode, types, ranks and monophyly: a response to Pickett

A report from the First International Phylogenetic Nomenclature Meeting recently published in Cladistics conveys several misconceptions about the PhyloCode and presents an erroneous interpretation of discussions that took place at that meeting. Contrary to Pickett's assertions, the PhyloCode is designed to name clades, not paraphyletic groups; the rejection of ranks has never been a fundamental principle of phylogenetic nomenclature; and specifiers under the PhyloCode differ in several ways from types under rank‐based nomenclature. © The Willi Hennig Society 2005.     

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.     

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.     

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.     

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.     

Ceci n'est pas une pipe: names, clades and phylogenetic nomenclature

An introduction is provided to the literature and to issues relating to phylogenetic nomenclature and the PhyloCode, together with a critique of the current Linnaean system of nomenclature. The Linnaean nomenclature fixes taxon names with types, and associates the names with ranks (genus, family, etc.). In phylogenetic nomenclature, names are instead defined with reference to cladistic relationships, and the names are not associated with ranks. We argue that taxon names under the Linnaean system are unclear in meaning and provide unstable group–name associations, notwithstanding whether or not there are agreements on relationships. Furthermore, the Linnaean rank assignments lack justification and invite unwarranted comparisons across taxa. On the contrary, the intention of taxon names in phylogenetic nomenclature is clear and stable, and the application of the names will be unambiguous under any given cladistic hypothesis. The extension of the names reflects current knowledge of relationships, and will shift as new hypotheses are forwarded. The extension of phylogenetic names is, therefore, clear but is associated to (and thus dependent upon) cladistic hypotheses. Stability in content can be maximized with carefully formulated name definitions. A phylogenetic nomenclature will shift the focus from discussions of taxon names towards the understanding of relationships. Also, we contend that species should not be recognized as taxonomic units. The term ‘species’ is ambiguous, it mixes several distinct classes of entities, and there is a large gap between most of the actual concepts and the evidence available to identify the entities. Instead, we argue that only clades should be recognized. Among these, it is useful to tag the smallest named clades, which all represent non-overlapping groups. Such taxa  – LITUs (Least Inclusive Taxonomic Units) – are distinguished from more inclusive clades by being spelled with lower-case initial letter. In contrast to species, LITUs are conceptually straightforward and are, like other clades, identified by apomorphies.     

Stems,nodes, crown clades,and rank‐free lists: is Linnaeus dead?

Recent radical proposals to overhaul the methods of biological classification are reviewed. The proposals of phylogenetic nomenclature are to translate cladistic phylogenies directly into classifications, and to define taxon names in terms of clades. The method has a number of radical consequences for biologists: taxon names must depend rigidly on the particular cladogram favoured at the moment, familiar names may be reassigned to unfamiliar groupings, Linnaean category terms (e.g. phylum, order, family) are abandoned, and the Linnaean binomen (e.g. Homo sapiens) is abandoned. The tenets of phylogenetic nomenclature have gained strong support among some vocal theoreticians, and rigid principles for legislative control of clade names and definitions have been outlined in the PhyloCode. The consequences of this semantic maelstrom have not been worked out. In pratice, phylogenetic nomenclature will bc disastrous, promoting confusion and instability, and it should be abandoned. It is based on a fundamental misunderstanding of the difference between a phylogeny (which is real) and a classification (which is utilitarian). Under the new view, classifications are identical to phlylogenies, and so the proponents of phylogenetic nomenclature will end up abandoning classifications altogether.     

Apomorphy-based definition also pinpoints a node, and PhyloCode names prevent effective communication

Acceptable methods of defining taxon (or clade) names in the draft PhyloCode, or so-called phylogenetic nomenclature, are “node based,” “stem based,” and “apomorphy based.” All of them define a clade name by pinpointing a node; whereas node-based and stem-based definitions require two or more taxon “specifiers” to define names, an apomorphy-based definition requires two specifiers of different types; namely, a single-taxon specifier and a character specifier. The taxon specifier in an apomorphy-based definition is completely different from the “type” in the Linnaean system. Taxon (or clade) names in the PhyloCode are characterized in two entirely different manners: One is a name that does not change, either in its orthography or in the contents of the taxon referred to by it (or its meaning) over time; the other is a name that is just like a pure mark and thus has no meaning. Communication through such PhyloCode names is very ineffective or impossible.     

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.     

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.     

Species names in phylogenetic nomenclature

Linnaean binomial nomenclature is logically incompatible with the phylogenetic nomenclature of de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449-480): The former is based on the concept of genus, thus making this rank mandatory, while the latter is based on phylogenetic definitions and requires the abandonment of mandatory ranks. Thus, if species are to receive names under phylogenetic nomenclature, a different method must be devised to name them. Here, 13 methods for naming species in the context of phylogenetic nomenclature are contrasted with each other and with Linnaean binomials. A fundamental dichotomy among the proposed methods distinguishes those that retain the entire binomial of a preexisting species name from those that retain only the specific epithet. Other relevant issues include the stability, uniqueness, and ease of pronunciation of species names; their capacity to convey phylogenetic information; and the distinguishability of species names that are governed by a code of phylogenetic nomenclature both from clade names and from species names governed by the current codes. No method is ideal. Each has advantages and drawbacks, and preference for one option over another will be influenced by one's evaluation of the relative importance of the pros and cons for each. Moreover, sometimes the same feature is viewed as an advantage by some and a drawback by others. Nevertheless, all of the proposed methods for naming species in the context of phylogenetic nomenclature provide names that are more stable than Linnaean binomials.     

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.     

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。     

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.     

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。     

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.     

The new and improved PhyloCode, now with types, ranks, and even polyphyly: a conference report from the First International Phylogenetic Nomenclature Meeting

A report from the first International Phylogenetic Nomenclature Meeting is presented. The meeting revealed that the PhyloCode, once implemented, will itself not require adherence to the three major tenets of philosophy that proponents have claimed required its creation. These include the abandonment of (1) non‐monophyletic taxa, (2) ranks, and (3) types. © The Willi Hennig Society 2005.     

Nomenclature for factors of the dog major histocompatibility system (DLA), 1998: first report of the ISAG DLA Nomenclature Committee

A Nomenclature committee for Factors of the Dog Major Histocompatibility System or Dog Leukocyte Antigen (DLA) has been convened under the auspices of the International Society for Animal Genetics (ISAG) to define a sequence based nomenclature for the genes of the DLA system. The remit of this committee includes: assignment of gene names rules for naming alleles assignment of names to published alleles assignment of names to new alleles rules for acceptance of new alleles DLA Nomenclature Committee, rules for acceptance, DLA genes and alleles, sequence based nomenclature.