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.     

Names,numbers and indentations: a guide to post-Linnaean taxonomy

The vast majority of biological taxonomists use the Linnaean system when constructing classifications. Taxa are assigned Linnaean ranks and taxon names are devised according to the Linnaean rules of nomenclature. Unfortunately, the Linnaean system has become theoretically outdated. Moreover, its continued use causes a number of practical problems. This paper begins by sketching the ontological and practical problems facing the Linnaean system. Those problems are sufficiently pressing that alternative systems of classification should be investigated. A number of proposals for an alternative system are introduced and evaluated. The best aspects of those proposals are brought together to form a post-Linnaean system, and a comparison of the Linnaean and post-Linnaean systems is conducted. The final section of this paper considers not only the theoretical reasons for replacing the Linnaean system, but also the practical feasibility of adopting an alternative system.     

A Higher Level Classification of All Living Organisms

We present a consensus classification of life to embrace the more than 1.6 million species already provided by more than 3,000 taxonomists’ expert opinions in a unified and coherent, hierarchically ranked system known as the Catalogue of Life (CoL). The intent of this collaborative effort is to provide a hierarchical classification serving not only the needs of the CoL’s database providers but also the diverse public-domain user community, most of whom are familiar with the Linnaean conceptual system of ordering taxon relationships. This classification is neither phylogenetic nor evolutionary but instead represents a consensus view that accommodates taxonomic choices and practical compromises among diverse expert opinions, public usages, and conflicting evidence about the boundaries between taxa and the ranks of major taxa, including kingdoms. Certain key issues, some not fully resolved, are addressed in particular. Beyond its immediate use as a management tool for the CoL and ITIS (Integrated Taxonomic Information System), it is immediately valuable as a reference for taxonomic and biodiversity research, as a tool for societal communication, and as a classificatory “backbone” for biodiversity databases, museum collections, libraries, and textbooks. Such a modern comprehensive hierarchy has not previously existed at this level of specificity.     

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.     

Classification of apocynaceae s.l. according to a new approach combining Linnaean and phylogenetic taxonomy

A new approach to a nomenclatural system, including elements from both Linnaean and phylogenetic nomenclature, is proposed. It is compatible with the existing Linnaean system, including "standard names" corresponding to principal and secondary ranks, and uses a variant of the definitions from the Phylocode system. A new infrafamilial classification, using this nomenclatural approach, of the Apocynaceae s.l. (i.e., including the Asclepiadaceae) based mainly on analyses of rbcL and ndhF data is discussed. Twenty-one tribes and four rankless taxa are defined.     

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.     

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.     

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.     

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.     

Naming diversity in an evolutionary context: Phylogenetic definitions of the Roucela clade (Campanulaceae/Campanuloideae) and the cryptic taxa within

In recent times, evolution has become a central tenet of taxonomy, but nomenclature has consistently been decoupled from the tree‐thinking process, often leading to significant issues in reconciling traditional (Linnaean) names with clades in the Tree of Life. Recent evolutionary studies on the Roucela clade, a group of endemic plants found in the Mediterranean Basin, motivated the establishment of phylogenetic concepts to formally anchor clade names on the Campanuloideae (Campanulaceae) tree. These concepts facilitate communication of clades that approximate traditionally defined groups, in addition to naming newly discovered cryptic diversity in a phylogenetic framework.     

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 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.     

Finite linnaean structures

This paper considers a class of set-theoretical entities, calledn-rank Linnaean structures, which are intended as abstract models of the taxonomic classificatory systems of biology. In the first part, devoted to formalism, finite Linnaean structures are discussed in complete generality; but, in addition, eight distinct subclasses are noted and some of the properties of their elements are explored. In the second part, concerned with applications, it is shown that taxonomic systems may be recast in the form of finite Linnaean structures, and an effort is made to show that some undesirable features of earlier models are avoided without artificiality and without abandoning extensional mathematics.     

The role of subspecies in obscuring avian biological diversity and misleading conservation policy

Subspecies are often used in ways that require their evolutionary independence, for example as proxies for units of conservation. Mitochondrial DNA sequence data reveal that 97% of continentally distributed avian subspecies lack the population genetic structure indicative of a distinct evolutionary unit. Subspecies considered threatened or endangered, some of which have been targets of expensive restoration efforts, also generally lack genetic distinctiveness. Although sequence data show that species include 1.9 historically significant units on average, these units are not reflected by current subspecies nomenclature. Yet, it is these unnamed units and not named subspecies that should play a major role in guiding conservation efforts and in identifying biological diversity. Thus, a massive reorganization of classifications is required so that the lowest ranks, be they species or subspecies, reflect evolutionary diversity. Until such reorganization is accomplished, the subspecies rank will continue to hinder progress in taxonomy, evolutionary studies and especially conservation.     

Defining phyla: morphological and molecular clues to metazoan evolution

None of the supraspecific taxonomic categories can be defined objectively. Each taxon should of course be monophyletic, but there is no morphological or molecular character that identifies, for example, the phylum level. This has led some authors to abandon the Linnaean categories, but they appear to be practical "handles" in daily communication. It has been proposed that each phylum exhibits a characteristic Bauplan, but the identification of such "types" have in practice proved difficult or impossible for several phyla. Monophyly of some of the approximately 30 morphology-based phyla has been put in question by molecular studies, but recent reports clearly show that the 18S rRNA molecule, which has been used extensively in phylogenetic analyses, cannot be used alone in identifying phyla (or other higher taxonomic groups). Some higher taxa, for example Chordata, Vertebrata, and Echinodermata, consistently show up as monophyletic in the analyses, whereas molluscan and annelidan subgroups just as consistently are mixed with each other and with a number of other protostomian phyla in varying patterns.     

PERSPECTIVE: EVOLUTIONARY PATTERNS IN THE FOSSIL RECORD

The study of large-scale evolutionary patterns in the fossil record has benefited from a diversity of approaches, including analysis of taxonomic data, ecology, geography, and morphology. Although genealogy is an important component of macroevolution, recent visions of phylogenetic analysis as replacing rather than supplementing other approaches are short-sighted. The ability of traditional Linnaean taxa to document evolutionary patterns is mainly an empirical rather than a theoretical issue, yet the use of these taxa has been dismissed without thorough evaluation of their empirical properties. Phylogenetic analysis can help compensate for some of the fossil record's imperfections. However, the shortcomings of the phylogenetic approach have not been adequately acknowledged, and we still lack a rigorous comparison between the phylogenetic approach and probabilistic approaches based on sampling theory. Important inferences about the history of life based on nongenealogical data have later been corroborated with genealogical and other analyses, suggesting that we risk an enormous loss of knowledge and understanding if we categorically dismiss nonphylogenetic data.     

ON SPECIES and OTHER TAXA

Abstract— It is argued that taxa, whether Linnaean or phylogenetic, belong to Popper's worlds 2 and 3, the worlds of knowledge, but that they represent entities residing in world 1, the world of objects, namely, classes of living beings. The Linnaean taxa are concepts, and thus untestable, whereas phylogenetic taxa are statements, the monophyletic taxa being true, and the paraphyletic and polyphyletic ones false statements. The taxa are neither strictly nor numerically universal statements, but probabilistic ones which cannot be falsified by single observations. It is suggested that the classical "species problem" is due to the fact that "species" has been used in three different senses. First, traditionally it has been assumed that the specific "essence" of an organism is that by which it is what it is. When we know the species, we know the organism. Second, the species are terminal taxa in the phylogenetic hierarchy. This implies that it is only a very small part of the "essence" of the organism which distinguishes the species. The remaining part characterizes the succession of superior taxa in the phylogenetic lineage which ends with the species in question. Third, the species has been regarded to be the "evolutionary unit." This idea may be refuted for two reasons: (1) since concepts and statements cannot evolve, species cannot evolve either, and (2) it is generally in very small isolated populations that evolutionary innovations are first established. In Linnean systematics the superior taxa are allotted categorical rank. The fact that the classification is constrained by this conventional stipulation implies that the superior taxa are often man-made artifacts. In the phylogenetic hierarchy, composed of monophyletic taxa, the ontological states of the taxa is completely independent of their numerical rank; the kingdom is as "real" as the species.     

The Linnaean Plant Name Typification Project

JARVIS, C. E., 1992. The Linnaean Plant Name Typification Project. Carl Linnaeus (1707–1778) introduced the consistent use of binomial names for plants and animals. As he published more than 9000 plant names, valid under the International Code of Botanical Nomenclature, their application is of considerable importance. Professor Steam's reputation as a Linnaean scholar brought him literally hundreds of requests, from all over the world, for help in the interpretation of Linnaean names. In 1980 he was instrumental in obtaining funding for a pilot study for the typification of Linnaean names. The Project was subsequently core-funded by the Natural History Museum, and has developed into an international Project that has attracted support and collaboration on a worldwide basis. The aims, methodology and progress of the Project are reviewed, and the names Crepis barbata L. and Hieracium capense L. are lectotypified.     

Lectotypifications of Lìnnaean names for Flora Nordica Vol. 1 (Lycopodiaceae — Papaveraceae)

Linnaean names appearing in Volume 1 of Flora Nordica are typified. The main sources for types are the Linnaean Herbarium (LINN), the Clifford Herbarium (BM), the Burser Herbarium (UPS) the Iter lapponicum Herbarium in Paris (LAPP), and cited illustrations. The study forms part of the "Linnaean Plant Name Typification Project" based at the Natural History Museum (BM). Flora Nordica notes no. 10.     

Taxonomic surrogacy in biodiversity assessments,and the meaning of Linnaean ranks

The majority of biodiversity assessments use species as the base unit. Recently, a series of studies have suggested replacing numbers of species with higher ranked taxa (genera, families, etc.); a method known as taxonomic surrogacy that has an important potential to save time and resources in assesments of biological diversity. We examine the relationships between taxa and ranks, and suggest that species/higher taxon exchanges are founded on misconceptions about the properties of Linnaean classification. Rank allocations in current classifications constitute a heterogeneous mixture of various historical and contemporary views. Even if all taxa were monophyletic, those referred to the same rank would simply denote separate clades without further equivalence. We conclude that they are no more comparable than any other, non‐nested taxa, such as, for example, the genus Rattus and the phylum Arthropoda, and that taxonomic surrogacy lacks justification. These problems are also illustrated with data of polychaetous annelid worms from a broad‐scale study of benthic biodiversity and species distributions in the Irish Sea. A recent consensus phylogeny for polychaetes is used to provide three different family‐level classifications of polychaetes. We use families as a surrogate for species, and present Shannon‐Wiener diversity indices for the different sites and the three different classifications, showing how the diversity measures rely on subjective rank allocations.