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.     

Brassicaceae: Species checklist and database on CD-Rom

A species checklist has been prepared for the Brassicaceae (Cruciferae) family, providing the first updated list in over 70 years. The family, currently, includes 338 genera and 3709 species. The database contains approximately 14,000 taxonomic names (records). Taxon status and synonymy, taxon name, scientific authority, literature source and source verification, and the basionym are provided for each record. Electronic supplementary material to this article is available at and is accessible for authorized users.     

Do we need a Unique Scientist ID for publications in biomedicine?

BACKGROUND: The PubMed database contains nearly 15 million references from more than 4,800 biomedical journals. In general, authors of scientific articles are addressed by their last name and forename initial. DISCUSSION: In general, names can be too common and not unique enough to be search criteria. Today, Ph.D. students, other researchers and women publish scientific work. A person may not only have one name but several names and publish under each name. A Unique Scientist ID could help to address people in peer-to-peer (P2P) networks. As a starting point, perhaps PubMed could generate and manage such a scientist ID. SUMMARY: A Unique Scientist ID would improve knowledge management in science. Unfortunately in some of the publications, and then within the online databases, only one letter abbreviates the author's forename. A common name with only one initial could retrieve pertinent citations, but include many false drops (retrieval matching searched criteria but indisputably irrelevant).     

The anArchive taxonomic Checklist for Italian botanical data banking and vegetation analysis: Theoretical basis and advantages

In recent years, research in botany was increasingly related with the use of large data-sets and data banks, in order to address emerging issues such as the severe risk of species, habitats and biodiversity loss. In this frame, the anArchive taxonomic Checklist, an online synonymized list of botanical species names, developed to support the botanical data banking and vegetation analysis, is presented and discussed here. The benefits deriving from such a supervised and referenced tool are emphasized. They include the possibility to keep track of old and new species names, pointing out the latest reviewed accepted scientific name and its synonyms, and harmonizing different taxonomic points of view. Furthermore, the list is open access and expert qualified customers can collaborate to its improvement. The basic unit of the taxonomic Checklist is an object including the taxon name at specific or, when present, infraspecific level; the taxonomic frame stops at the level of family and ranks higher than genus are not treated hierarchically. Some technical features, the main taxonomic references and the current state of the art are reported.     

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.     

Taxamatch,an Algorithm for Near (‘Fuzzy’) Matching of Scientific Names in Taxonomic Databases

Misspellings of organism scientific names create barriers to optimal storage and organization of biological data, reconciliation of data stored under different spelling variants of the same name, and appropriate responses from user queries to taxonomic data systems. This study presents an analysis of the nature of the problem from first principles, reviews some available algorithmic approaches, and describes Taxamatch, an improved name matching solution for this information domain. Taxamatch employs a custom Modified Damerau-Levenshtein Distance algorithm in tandem with a phonetic algorithm, together with a rule-based approach incorporating a suite of heuristic filters, to produce improved levels of recall, precision and execution time over the existing dynamic programming algorithms n-grams (as bigrams and trigrams) and standard edit distance. Although entirely phonetic methods are faster than Taxamatch, they are inferior in the area of recall since many real-world errors are non-phonetic in nature. Excellent performance of Taxamatch (as recall, precision and execution time) is demonstrated against a reference database of over 465,000 genus names and 1.6 million species names, as well as against a range of error types as present at both genus and species levels in three sets of sample data for species and four for genera alone. An ancillary authority matching component is included which can be used both for misspelled names and for otherwise matching names where the associated cited authorities are not identical.     

我国进境检疫性菌物名录亟待修订完善

中华人民共和国现行进境检疫性菌物名录中共有130种。近年来由于菌物分类研究的快速发展,许多检疫性菌物的分类地位已经发生变化。本文对我国进境检疫性菌物名录中的名称与国际公认的分类体系和现用名进行了初步的比较和分析,进一步以茎点霉属和轮枝菌属为例说明分类系统的变化对菌物名称的影响。另外,名录中很多汉语学名的使用也不符合规范。我国进境检疫性菌物名录亟需修订。     

Cladistic information in phylogenetic definitions and designated phylogenetic contexts for the use of taxon names

A phylogenetic definition of a taxon name associates that name with a clade through its reference to a particular ancestor and all of its descendants. Depending on one's perspective, phylogenetic definitions name either clades on the one true, but unknown, phylogeny, or components on cladograms (clades on hypotheses regarding the true phylogeny). Phylogenetic definitions do not contain enough information to identify components without a reference cladogram. As a result, (1) if clades are equated with components on cladograms, a phylogenetic definition may associate a taxon name with different clades on different cladograms, and (2) the inclusiveness, diagnostic synapomorphies, and distribution in time and space of the clade with a particular name can differ markedly depending on the phylogenetic hypothesis one chooses to adopt. This potentially unacceptable lability in the clade to which a name refers can be avoided by using a taxon name in conjunction with only phylogenetic hypotheses on which specific taxa are related in a particular fashion. This designated phylogenetic context can be described in an n-taxon statement that would be appended to the phylogenetic definition. Use of the taxon name would be considered inappropriate in conjunction with cladograms on which the relationships contradict those in the n-taxon statement. Whereas phylogenetic definitions stabilize the meaning of taxon names, designated phylogenetic contexts would stabilize the usage of those names.     

Thermophilic fungi and applied research: a synopsis of name changes and synonymies

The present synopsis reports on taxonomic decisions and name changes introduced in the last decades for a number of thermophilic fungi. Taxa dealt with are those most commonly cited in the literature of fundamental and applied work or concern species having complex taxonomic histories. The definition of a thermophile follows the classificatory scheme elaborated by Cooney & Emerson in 1964. The synopsis provides the latest legal valid names for several thermophiles. Binomials of accepted synonymies are also reported with arguments in favour of these taxonomic decisions. The material of this contribution is a synthetic simplified account of two previous reviews on the taxonomy of thermophilic fungi. The present document aims: (1) to suppress the use of ghost binomials having no status of any kind; (2) to favour the continuous use of the latest legal valid name of a taxon to avoid cases of redundancies by citing binomials of known synonyms. Homogeneity in cited names is a fundamental prerequisite for comparative studies. The synopsis is thus a sound tool for future critical reviews of ecological and of biotechnological interests. The status of over a hundred names are here reviewed. Two additional new synonyms are proposed; these concern Mucor miehei var. minor and Sporotrichum cellulophilum. This revised version was published online in November 2006 with corrections to the Cover Date.     

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.     

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.     

Aphyly: A Systematic Designation for a Taxonomic Problem

A taxon is aphyletic when it is deemed to be non-monophyletic or unresolved, therefore aphyletic taxa are a taxonomic problem rather than an evolutionary anomaly. A problem arises in systematics when taxonomic names assigned to aphyletic taxa are treated as if they were natural groups. In the absence of a taxonomic and systematic revision, anomalous taxa should be labelled as aphyletic without recourse to phylogenetic inference (i.e., interpretation). Doing so avoids the validation of aphyletic names and the creation of dubious results in fields that rely on systematic and taxonomic data.     

A warning for ecologists and conservation biologists using species checklists: How the European marine fauna ‘lost’ all of its 16 <Emphasis Type="Italic">Discodoris</Emphasis> species (Mollusca: Gastropoda)

The European marine fauna used to be considered to include 16 species of Discodoris sea slugs until a recent worldwide revision demonstrated that there is not a single Discodoris species in European waters. This exemplary case illustrates the fact that species checklists do not accurately represent biodiversity unless they are based on sound taxonomic work in which (1) the status of every available species name has been addressed, i.e. whether it is valid, synonymous, or of doubtful application, and (2) classification reflects phylogenetic relationships. It is argued that taxonomic revisions are critically needed, because the status of species names can only be addressed properly through revisions. It is discussed that fields which depend on taxonomic data, such as conservation biology and ecology, might be affected deeply if problematic species names (synonyms and nomina dubia) have not been recognized. Consequently, it is proposed that a taxon that has not been revised be red-flagged in checklists, so that non-taxonomists will know which species names should be applied with caution or not at all.     

A taxonomic revision of Encyclia (Orchidaceae: Laeliinae) in Costa Rica

A taxonomic revision of Encyclia (Orchidaceae) in Costa Rica is presented. The taxonomic history of the genus and its phylogenetic position are discussed. Characters of vegetative and floral morphology are described and their taxonomic significance is discussed. The genus is treated as comprising nine species in the country and a key to species is provided. Each taxon is described on the basis of Costa Rican material, illustrated in a composite plate, and its distribution within the country is assessed. Distribution maps for all the taxa are given. Overall distribution, derivation of name, synonymy, notes on species ecology and diagnostic features are presented for each taxon. The names Encyclia tonduziana and Epidendrum mooreanum are typified. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 395–448.     

A Standardized Reference Data Set for Vertebrate Taxon Name Resolution

Taxonomic names associated with digitized biocollections labels have flooded into repositories such as GBIF, iDigBio and VertNet. The names on these labels are often misspelled, out of date, or present other problems, as they were often captured only once during accessioning of specimens, or have a history of label changes without clear provenance. Before records are reliably usable in research, it is critical that these issues be addressed. However, still missing is an assessment of the scope of the problem, the effort needed to solve it, and a way to improve effectiveness of tools developed to aid the process. We present a carefully human-vetted analysis of 1000 verbatim scientific names taken at random from those published via the data aggregator VertNet, providing the first rigorously reviewed, reference validation data set. In addition to characterizing formatting problems, human vetting focused on detecting misspelling, synonymy, and the incorrect use of Darwin Core. Our results reveal a sobering view of the challenge ahead, as less than 47% of name strings were found to be currently valid. More optimistically, nearly 97% of name combinations could be resolved to a currently valid name, suggesting that computer-aided approaches may provide feasible means to improve digitized content. Finally, we associated names back to biocollections records and fit logistic models to test potential drivers of issues. A set of candidate variables (geographic region, year collected, higher-level clade, and the institutional digitally accessible data volume) and their 2-way interactions all predict the probability of records having taxon name issues, based on model selection approaches. We strongly encourage further experiments to use this reference data set as a means to compare automated or computer-aided taxon name tools for their ability to resolve and improve the existing wealth of legacy data.     

Review of ‘The Plant List,a working list of all plant species’

The Plant List ( http://www.theplantlist.org/ ) is an on‐line database of plant names that aims to be comprehensive for all described plant species. Version 1 of The Plant List includes 1 040 426 plant name records, of which 298 900 are accepted names. The Plant List is the product of a consortium of the Royal Botanic Gardens, Kew, and the Missouri Botanical Garden. In this review, I evaluate the use of this plant taxonomic database for plant ecologists. The web interface of The Plant List allows a quick search for species names and corresponding synonyms. Moreover, users are able to download search or browse results to compile a customized checklist of plant names. The combination of a straightforward web design and the possibility to download search results provides a valuable resource of plant nomenclature information for a wide range of plant ecologists.