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.     

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.     

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.     

A logic approach to modelling nomenclatural change

We utilize an Answer Set Programming (ASP) approach to show that the principles of nomenclature are tractable in computational logic. To this end we design a hypothetical, 20 nomenclatural taxon use case, with starting conditions that embody several overarching principles of the International Code of Zoological Nomenclature, including Binomial Nomenclature, Priority, Coordination, Homonymy, Typification and the structural requirement of Gender Agreement. The use case ending conditions are triggered by the reinterpretation of the diagnostic features of one of 12 type specimens anchoring the corresponding species‐level epithets. Permutations of this child‐to‐parent reassignment action lead to 36 alternative scenarios, where each scenario requires a set of 1–14 logically contingent nomenclatural emendations. We show that an ASP transition system approach can correctly infer the Code‐mandated changes for each scenario, and visually output the ending conditions. The results provide a foundation for further developing logic‐based nomenclatural change optimization and validation services, which could be applied in global nomenclatural registries. More generally, logic explorations of nomenclatural and taxonomic change scenarios provide a novel means of assessing design biases inherent in the principles of nomenclature, and can therefore inform the design of future, big data‐compatible identifier systems that recognize and mitigate these constraints.     

The why and how of determining length-weight relationships of fish from preserved museum specimens

The rationale and a strategy for the estimation of length-weight relationships (LWR) using preserved specimens of less common fish species in museums is presented, along with preliminary results pertaining to 56 specimens and 31 species of fish from the Australian Museum, Sydney, Australia, the Marine Biological Specimen Museum of Chinese Academy of Sciences in Qingdao, China, and the Beaty Biodiversity Museum of the University of British Columbia, Vancouver, Canada. These results are discussed in the context of the effects of seasonality (in fresh specimens) and preservation (in museum specimens) on the estimation of LWR parameters.     

Phylogenetic definitions and taxonomic philosophy

An examination of the post-Darwinian history of biological taxonomy reveals an implicit assumption that the definitions of taxon names consist of lists of organismal traits. That assumption represents a failure to grant the concept of evolution a central role in taxonomy, and it causes conflicts between traditional methods of defining taxon names and evolutionary concepts of taxa. Phylogenetic definitions of taxon names (de Queiroz and Gauthier 1990) grant the concept of common ancestry a central role in the definitions of taxon names and thus constitute an important step in the development of phylogenetic taxonomy. By treating phylogenetic relationships rather than organismal traits as necessary and sufficient properties, phylogenetic definitions remove conflicts between the definitions of taxon names and evolutionary concepts of taxa. The general method of definition represented by phylogenetic definitions of clade names can be applied to the names of other kinds of composite wholes, including populations and biological species. That the names of individuals (composite wholes) can be defined in terms of necessary and sufficient properties provides the foundation for a synthesis of seemingly incompatible positions held by contemporary individualists and essentialists concerning the nature of taxa and the definitions of taxon names.     

Should taxon names be explicitly defined?

Overviews are provided for traditional and phylogenetic nomenclature. In traditional nomenclature, a name is provided with a type and a rank. In the rankless phylogenetic nomenclature, a taxon name is provided with an explicit phylogenetic definition, which attaches the name to a clade. Linnaeus’s approach to nomenclature is also reviewed, and it is shown that, although the current system of nomenclature does use some Linnaean conventions (e.g., certain rank-denoting terms, binary nomenclature), it is actually quite different from Linnaean nomenclature. The primary differences between traditional and phylogenetic nomenclature are reviewed. In phylogenetic nomenclature, names are provided with explicit phylogenetic definitions, whereas in traditional nomenclature names are not explicitly defined. In phylogenetic nomenclature, a name remains attached to a clade regardless of how future changes in phylogeny alter the clade’s content; in traditional nomenclature a name is not “married” to any particular clade. In traditional nomenclature, names must be assigned ranks (an admittedly arbitrary process), whereas in phylogenetic nomenclature there are no formal ranks. Therefore, in phylogenetic nomenclature, the name itself conveys no hierarchical information, and the name conveys nothing regarding set exclusivity. It is concluded that the current system is better able to handle new and unexpected changes in ideas about taxonomic relationships. This greater flexibility, coupled with the greater information content that the names themselves (i.e., when used outside the context of a given taxonomy or phytogeny) provide, makes the current system better designed for use by all users of taxon names.     

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.     

Species delimitation methods reveal cryptic diversity in the Hypnea cornuta complex (Cystocloniaceae,Rhodophyta)

The simple and convergent morphologies of many red algae make these species difficult to identify using traditional morphological characters. Many cryptic species have been described in recent years based on molecular datasets, and this has led to the application of an integrative taxonomy approach in species delimitation. Here, we performed several species delimitation methods (mBGD, ABGD, SPN, PTP, GMYCs and GMYCm) based on two different loci (COI-5P and rbcL) in species of the Hypnea cornuta complex. These methods were combined with morphological and phylogenetic data, extensive sampling, analysis of topotype material, and historically relevant herbarium samples. Our findings demonstrate that the groups morphologically assigned to H. cornuta and H. stellulifera consist of five different cryptic species. H. cornuta is a polyphyletic taxon composed of three well-separated lineages, thus requiring sequencing of type or topotype specimens to determine which one is Hypnea cornuta sensu stricto. We have revealed that the distribution of H. stellulifera is limited to Asia, while the Brazilian specimens initially assigned to this species were clarified as a new endemic species: Hypnea cryptica sp. nov. Our results indicated that only an integrative approach combining several lines of evidence, including morphology, nomenclature history, molecular data, biogeography and ecology can correctly solve the taxonomic status of widely distributed cryptic species.     

Homalothecium meridionale (M.Fleisch. & Warnst.) Hedenäs: a distinct species from H. sericeum (Hedw.) Schimp. (Brachytheciaceae,Bryopsida) in the Iberian Peninsula

Previous molecular studies have done much to shed some light on the taxonomy and phytogeographic position of Homalothecium sericeum and H. meridionale and the present study clarifies the taxonomy and distribution of the two species across Iberia. By conducting a revision of Homalothecium specimens available in Spanish and Portuguese herbaria, we concluded that sporophytic differences are the most appropriate characters for the delimitation of each species. Scanning electron microscope examination of the peristomes of the two taxa helped distinguish between them.

We also noted that H. meridionale is a frequently distributed taxon throughout the Iberian territory, but occurs mostly in Portuguese areas with a Mediterranean influence, becoming less frequent in the Atlantic as well as in continental parts of the Peninsula. As a result of this study, based on numerous new localities in Portugal and Spain, we provide an updated map of the distribution of H. meridionale, and an account of its ecology and habitat affinities.     

西双版纳傣族民间植物命名与分类系统研究

西双版纳傣族民间对植物的命名采用了“双名”法。他们的“属”概念包含了植物的生活型和经济型;而“种名”则根据植物的特征、特性、用途、产地和生境等加以描述,有较高的实用价值。此外,按照傣族对植物的概念与命名,本研究建立了一个傣族民间植物的分类系统。     

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.     

Tarsius lariang: A New Primate Species from Western Central Sulawesi

On the basis of morphological, anatomical, and acoustic analyses, the tarsiers of the Gimpu region on Sulawesi belong to a previously undescribed species of the genus Tarsius Storr, 1780. We describe the new taxon as Tarsius lariang new species. In November 2001, S. Merker collected 8 specimens of Tarsius lariang near Gimpu, Central Sulawesi, Indonesia. Four of them were transferred to the Indonesian Institute of Sciences at Cibinong to be held in an enclosure, and after their deaths become part of the collection of the Museum Zoologicum Bogoriense, Bogor. The new species is distinctive in pelage, skull, and body proportions, and in vocalization. We describe the unique territorial duet song characteristic for them and place the taxon into a biogeographic framework developed in previous studies.     

Ontology of evolution and methodology of taxonomy

The theoretical basis of evolutionary biology is presented and discussed to introduce the reader to problems of evolutionary theory and particularly to the problem of paradigm selection. Advantages of the epigenetic hypothesis over the synthetic one are demonstrated, and a wide array of inferences is analyzed including the hypothesis of adaptive trade-off, which considers the organism as a finely tuned comprehensive whole that is restricted in modification unless under more or less serious destabilization. The basic premises of phylogenetics, taxonomy, and taxonomic nomenclature are also analyzed; this results in the inference that the phyletic (refined traditional, Linnean) methodology has advantages over the cladistic one. The nature of the biological taxon and the problems of taxonomy of taxonomically imperfect material (paleontological, parasitological, etc.) are discussed.     

Redescription of the fish parasite Lernanthropus polynemi Richiardi, 1881 (Copepoda: Siphonostomatoida) and relegation of two congeners to synonymy

Lernanthropus polynemi Richiardi, 1881 is described, for the first time since its original discovery, based on the type-material found in the Museum für Naturkunde in Berlin, Germany. Morphological features of this parasite, which infects the commercially-caught fish Eleutheronema tetradactylum (Shaw), are described and illustrated, including those of the male, which is described for the first time. The types of another species from the same host, L. lappaceus Wilson, 1912, and deposited in the National Museum of Natural History in Washington DC, are also examined based on the type-specimens. The types of a third congener, L. trifoliatus Basset-Smith, 1898, also from the same host, are not available, but the original illustrations are studied. It is considered that the three nominal species described from E. tetradactylum represent a single taxon, and that L. lappaceus and L. trifoliatus be relegated to synonymy with L. polynemi.     

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.     

Linnaean fish specimens in the Swedish Museum of Natural History, Stockholm

Specimens of fish in the Naturhistoriska riksmuseet, Stockholm, which are type specimens of species described by Linnaeus are listed. A total of 94 taxa is represented in the collection. The sources for the typification of each taxon are given and the existence of type material in other collections is noted. A short history of this collection of fishes is given as it relates to confirmation of the original nature of the specimens.
Most of the taxa represented came from the collection of King Adolf Fredrik (1710–1771) and were described by Linnaeus in the Museum Adolphi Friderici Volumes 1 and 2 (1754a, 1764) or from Fredrick Hasselqvist's (1722–1752) collections in North Africa and the Mediterranean borderlands.     

中国东北牻牛儿苗科（Geraniaceae）花粉形态与系统分类学研究

本文对中国东北牛儿苗科Ｇｅｒａｎｉａｃｅａｅ老鹳草属Ｇｅｒａｎｉｕｍ和牛儿苗属Ｅｒｎｄｉｕｍ植物计２属,１４种,２变种及１变型的花粉形态进行了较系统的研究。并对本科花粉形态进行了分类处理,编制了花粉形态科种检索表。结果表明,本科花粉如按萌发孔类型、外壁雕纹式样可以分为二大类：即三孔沟,外壁雕纹瘤状（Ｇｅｒａｎｉｕｍ）三沟,外壁雕纹网状（Ｅｒｏｄｉｕｍ）。在老鹳草属种及种下等级的分类处理中,花粉粒大小、萌发沟长度、外壁覆盖层网眼均匀性、直径大小、网脊上纹饰及外壁雕纹瘤纹突起均匀性、大小及瘤上纹饰都具有较大的分类学意义。花粉形态分类与经典分类对本科分类群的处理意见相吻合。大大丰富了本科分类微形态的证据。