Constraints in naming parts of the Tree of Life

Dayrat, B. & Gosliner, T. M. (2005). Species names and metaphyly: a case study in Discodorididae (Mollusca, Gastropoda, Euthyneura, Nudibranchia, Doridina) —Zoologica Scripta, **, ***–***.Absence of resolution in phylogenetic trees, or metaphyly, is a common phenomenon. It mainly results from the fact that each data set has its own limit and can hardly be expected to reconstruct alone an entire hierarchy. Because metaphyly helps point out which regions of a tree merit further investigation, one should not avoid metaphyly but rather should try to detect it by addressing carefully node reliability. In this paper we explore the implication of metaphyly for species names. We present a phylogenetic analysis of Discodorididae (Mollusca, Gastropoda, Nudibranchia, Doridina), with an emphasis on relationships among species of Discodoris and its traditionally close ‘allies’ such as Peltodoris and Anisodoris. We demonstrate that some species must be transferred to different discodoridid subclades with which they share synapomorphies, but that many species form a metaphyletic group at the base of Discodorididae, and therefore cannot be placed in any taxon of genus level. We demonstrate that the current International Code of Zoological Nomenclature does not allow taxonomists to handle this situation because it requires selecting a taxon name of genus rank for every species binomial. Then we evaluate the results provided by new forms of species names, both in a rank‐based system, such as the current nomenclature, and a rank‐free system. All solutions considered would cause radical changes to the ‘spirit’ of the current ICZN (and, by extension, to the other current codes). In a rank‐free system of nomenclature, such as the PhyloCode, the best result is obtained with an epithet‐based form that does not mention supra‐specific relationships. Under this method, official species names would take the form ‘boholiensis Bergh, 1877’, although page numbers and letters can be added for uniqueness purposes. Taxonomists would then be free to add supra‐specific taxon names in ‘common’ species names, such as Discodorididae boholiensis Bergh, 1877 or simply Discodorididae boholiensis. Here we wish to stimulate discussion of a problem that we believe merits wide debate: absence of resolution in phylogenetic reconstruction and its impact on species nomenclature.

NOMENCLATURE OF CULTIVATED PLANTS: A HISTORICAL BOTANICAL STANDPOINT

This book inventories all available (and some unavailable) names in the family, genus, and species groups of extant members of orders Actiniaria and Corallimorpharia [cnidarian subclass Hexacorallia (Zoantharia) of class Anthozoa], providing a benchmark of names, their status, and taxon membership. I have attempted to make the compilation complete as of 2010; some names created after 2010 are included. The book is derived from a database I compiled that was available through a website. Most of the book is from the literature that defines taxa and documents their geographic distribution-primarily publications on nomenclature, taxonomy, and biogeography, but also some on ecology, pharmacology, reproductive biology, physiology, etc. of anemones (the common name for these groups); the reference section comprises 845 entries. As for previous anemone catalogs, this contains taxonomic as well as nomenclatural information, the former based on subjective opinion of working biologists, the latter objectively verifiable and unchanging (except by action of the International Commission on Zoological Nomenclature). Each family-group name, genus-group name, and original combination for species-group names has an entry. The entry contains the bibliographic reference to the publication in which each name was made available. This book contains for Corallimorpharia seven family names (four considered valid [57%]), 20 generic names (10 considered valid [50%] and one unavailable), and 65 species names (46 considered valid [70%]). It contains for Actiniaria 86 family names (50 considered valid [58%] and three unavailable), 447 generic names (264 considered valid [59%] and two unavailable), and 1427 species names (1101 considered valid [77%] and nine unavailable). Type specimens are inventoried from more than 50 natural history museums in Africa, Australia, Europe, New Zealand, and North America, including those with the largest collections of anemones; the geographic sources of specimens that were the bases of new names are identified. I resolve some nomenclatural issues, acting as First Reviser. A few taxonomic opinions are published for the first time. I have been unable to resolve a small number of problematic names having both nomenclatural and taxonomic problems. Molecular phylogenetic analyses are changing assignment of genera to families and species to genera. Systematics may change, but the basics of nomenclature remain unchanged in face of such alterations. All actions are in accord with the principles of nomenclature enunciated in the International Code of Zoological Nomenclature. These include the type concept, the Principle of Coordination, and the Principle of Priority. Nomenclatural acts include the creation of new replacement names; seven actiniarian generic names and one species name that are junior homonyms but have been treated as valid are replaced and an eighth new genus name is created. I designate type species for two genera. Except for published misspellings, names are rendered correctly according to the International Code of Zoological Nomenclature; I have altered spelling of some species names to conform to orthographic regulations. I place several species that had been assigned to genera now considered junior synonyms in the genus to which the type species was moved; experts on these anemones should determine whether those generic placements, which follow the nomenclatural rules, are taxonomically appropriate. This inventory can be a useful starting point in assembling the literature and trying to understand the rationale for the creation and use of names for the taxonomic matters yet to be resolved. Some nomenclatural conundra will not be resolved until taxonomic uncertainties are. A taxonomist familiar with the animals needs to ascertain whether the published synonymies are justified. If so, the senior synonym should be used, which, in many instances, will involve determining the proper generic assignment of the species and the correct rendering of the name; if changing the name would be disruptive, retaining the junior name would require an appeal to the Commission (Code Article 23.11).

Biological type specimens are a particular kind of voucher specimen stored in natural history collections. Their special status and practical use are discussed in relation to the description and naming of taxonomic zoological diversity. Our current system, known as Linnaean nomenclature, is governed by the International Code of Zoological Nomenclature. The name of a species is fixed by its name-bearing type specimen, linking the scientific name of a species to the type specimen first designated for that species. The name-bearing type specimen is not necessarily a typical example of the species, while establishment of the boundaries of a species requires empirical taxonomic studies. The International Code of Zoological Nomenclature allows for the naming of new species in the absence of preserved specimens. However, photos and DNA sequences should not function as primary type material, while new species should not be described and named without deposition of at least one type specimen in a collection. Philosophically, species are individuals, spatiotemporally restricted entities. Therefore, Linnaean species names are proper names, which do not define the taxon but serve as a label, providing an ostensive definition of a species. Paratypes have no name-bearing function but, nevertheless, are highly valued specimens in natural history collections. Paratypes should be restricted to those specimens originating from the same sample as the holotype. Diagnosis of a species taxon involves establishment of a connection between a Linnaean name and determination of the boundaries of the species. A first step in this process is the choice of an appropriate species concept. It is not the examination of holotypes and paratypes that necessarily provides the best estimate of the taxonomic boundaries of a species, but this is facilitated by a set of voucher specimens known as the hypodigm. Dissatisfaction with the present nomenclatural code led some researchers to propose emendations. Other taxonomists suggested abandoning Linnaean nomenclature and proposed the alternative PhyloCode, albeit that it relegates the naming of species taxa to the traditional nomenclatural codes.

Zoologica ScriptaVolume 36, Issue 6 p. 623-623 Free Access Corrigendum This article corrects the following: Notothrix halsei gen. n., sp. n., representative of a new family of freshwater cladocerans (Branchiopoda, Anomopoda) from SW Australia, with a discussion of ancestral traits and a preliminary molecular phylogeny of the order Kay Van Damme, Russell J. Shiel, H. J. Dumont, Volume 36Issue 5Zoologica Scripta pages: 465-487 First Published online: September 4, 2007 First published: 01 October 2007 https://doi.org/10.1111/j.1463-6409.2007.00304.xCitations: 2AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Gondwanotrichidae nom. nov. pro Nototrichidae Van Damme, Shiel & Dumont, 2007 The authors (Van Damme et al.) of the paper ‘Notothrix halsei gen. n., sp. n., representative of a new family of freshwater cladocerans (Branchiopoda, Anomopoda) from SW Australia, with a discussion of ancestral traits and a preliminary molecular phylogeny of the order’ have alerted us to an error in their paper. The correction follows: In the previous issue of Zoologica Scripta [36(5): 465–487], we described a new monotypic family of Anomopoda (Crustacea: Branchiopoda) from SW Australia and named it as the Nototrichidae. However, the name of the type genus Notothrix Van Damme, Shiel & Dumont, 2007 turns out to be a junior homonym of the turbellarian genus Notothrix Hickman, 1955. Although the taxon described by Hickman (1955) was later synonymized with Umagilla Wahl, 1909 (Cannon 1987), this name remains available and therefore Notothrix Van Damme, Shiel & Dumont, 2007 is a junior homonym. As Notothrix Van Damme, Shiel & Dumont, 2007 is the type genus of the Nototrichidae Van Damme, Shiel & Dumont, 2007, the family name too becomes invalid, according to Article 39 of the International Code of Zoological Nomenclature (1999): ‘The name of a family group taxon is invalid if the name of its type genus is a junior homonym ...’. There are no synonyms for the type genus of the Nototrichidae. Therefore, we propose a new replacement name (nomen novum) for both the genus and the family. This is a strict nomenclatural issue that has further no effects on the content of the original paper. Family Gondwanotrichidae nom. nov. pro Nototrichidae Van Damme, Shiel & Dumont, 2007; diagnosis and description as in original publication. Type genus. Gondwanothrix nom. nov. pro Notothrix Van Damme, Shiel & Dumont, 2007 non Hickman, 1955. Type species. Notothrix halsei Van Damme, Shiel & Dumont, 2007. = Gondwanothrix halsei (Van Damme, Shiel & Dumont, 2007). Etymology. The name ‘Gondwanothrix’ consists of the prefix ‘Gondwano-’, referring to Gondwanaland, the supercontinent of the southern hemisphere that existed until its break-up in the Mesozoic, as we believe that this is one of the most primitive extant anomopods, dating back at least to that era (Van Damme et al. 2007). The word ‘thrix’ refers to the long setae on the posteroventral valve corner and the long spines on the postabdomen; the epitheton ‘halsei’ remains. Acknowledgements The authors wish to thank Steve Tracey and Dr Andrew Polaszek at the ICZN Secretariat for help and constructive advice. References Cannon, L. R. G. (1987). Two new rhabdocoel turbellarians, Umagilla pacifica sp. n. and U. karlingi sp. n. (Umagillidae), endosymbiotic with holothurians (Echinodermata) from the Great Barrier Reef and a discussion of sclerotic structures in the female system of the Umagillidae. Zoologica Scripta, 16 (4), 297– 303. Wiley Online LibraryWeb of Science®Google Scholar Hickman, V. V. (1955). Two new rhabdocoel turbellarians parasitic in Tasmania holothurians. Proceedings of the Royal Society of Tasmania, 89, 81– 97. Google Scholar International Commission on Zoological Nomenclature (1999). International Code of Zoological Nomenclature, 4th edn. Published by the International Trust for Zoological Nomenclature, c/o The Natural History Museum, London, UK. URL: http://www.iczn.org/iczn/index.jsp . Google Scholar Van Damme, K., Shiel, R. J. & Dumont, H. J. (2007). Notothrix halsei gen. n., sp. n., representative of a new family of freshwater cladocerans (Branchiopoda, Anomopoda) from SW Australia, with a discussion of ancestral traits and a preliminary molecular phylogeny of the order. Zoologica Scripta, 36 (5), 465– 487. Wiley Online LibraryWeb of Science®Google Scholar Citing Literature Volume36, Issue6November 2007Pages 623-623 ReferencesRelatedInformation

We are now over four decades into digitally managing the names of Earth's species. As the number of federating (i.e., software that brings together previously disparate projects under a common infrastructure, for example TaxonWorks) and aggregating (e.g., International Plant Name Index, Catalog of Life (CoL)) efforts increase, there remains an unmet need for both the migration forward of old data, and for the production of new, precise and comprehensive nomenclatural catalogs. Given this context, we provide an overview of how TaxonWorks seeks to contribute to this effort, and where it might evolve in the future. In TaxonWorks, when we talk about governed names and relationships, we mean it in the sense of existing international codes of nomenclature (e.g., the International Code of Zoological Nomenclature (ICZN)). More technically, nomenclature is defined as a set of objective assertions that describe the relationships between the names given to biological taxa and the rules that determine how those names are governed. It is critical to note that this is not the same thing as the relationship between a name and a biological entity, but rather nomenclature in TaxonWorks represents the details of the (governed) relationships between names. Rather than thinking of nomenclature as changing (a verb commonly used to express frustration with biological nomenclature), it is useful to think of nomenclature as a set of data points, which grows over time. For example, when synonymy happens, we do not erase the past, but rather record a new context for the name(s) in question. The biological concept changes, but the nomenclature (names) simply keeps adding up. Behind the scenes, nomenclature in TaxonWorks is represented by a set of nodes and edges, i.e., a mathematical graph, or network (e.g., Fig. 1). Most names (i.e., nodes in the network) are what TaxonWorks calls "protonyms," monomial epithets that are used to construct, for example, bionomial names (not to be confused with "protonym" sensu the ICZN). Protonyms are linked to other protonyms via relationships defined in NOMEN, an ontology that encodes governed rules of nomenclature. Within the system, all data, nodes and edges, can be cited, i.e., linked to a source and therefore anchored in time and tied to authorship, and annotated with a variety of annotation types (e.g., notes, confidence levels, tags). The actual building of the graphs is greatly simplified by multiple user-interfaces that allow scientists to review (e.g. Fig. 2), create, filter, and add to (again, not "change") the nomenclatural history. As in any complex knowledge-representation model, there are outlying scenarios, or edge cases that emerge, making certain human tasks more complex than others. TaxonWorks is no exception, it has limitations in terms of what and how some things can be represented. While many complex representations are hidden by simplified user-interfaces, some, for example, the handling of the ICZN's Family-group name, batch-loading of invalid relationships, and comparative syncing against external resources need more work to simplify the processes presently required to meet catalogers' needs. The depth at which TaxonWorks can capture nomenclature is only really valuable if it can be used by others. This is facilitated by the application programming interface (API) serving its data (https://api.taxonworks.org), serving text files, and by exports to standards like the emerging Catalog of Life Data Package. With reference to real-world problems, we illustrate different ways in which the API can be used, for example, as integrated into spreadsheets, through the use of command line scripts, and serve in the generation of public-facing websites. Behind all this effort are an increasing number of people recording help videos, developing documentation, and troubleshooting software and technical issues. Major contributions have come from developers at many skill levels, from high school to senior software engineers, illustrating that TaxonWorks leads in enabling both technical and domain-based contributions. The health and growth of this community is a key factor in TaxonWork's potential long-term impact in the effort to unify the names of Earth's species.

Thirty new species of benthic leptothecate hydroids were described and named from Patagonia in a 1991 PhD dissertation by Mohamed El Beshbeeshy. Although constituting nomina nuda under provisions of the International Code of Zoological Nomenclature (ICZN), the names of some species were used in several scientific publications between 1991 and 2011. In 2011, the dissertation of El Beshbeeshy was published in accordance with Article 8 of the ICZN. Several species-group names appearing in that work nevertheless fail to fully comply with certain articles of the code. The goal of this contribution is to review the nomenclatural availability of the names of those 30 new taxa, and to clearly establish the current status of El Beshbeeshy's material. Two of them were made available in 1999 as part of studies other than those of El Beshbeeshy, and correct authorship and date is here noted. Twenty-one of the nomina nuda were made available in a work published by El Beshbeeshy in 2011, although some constitute junior synonyms. Six of the new species-group names appearing in both the 1991 and 2011 works, established following a literature review of Patagonian species, were proposed without re-description, or designation of name-bearing types, or locations of such types. Most of them do not meet criteria of availability and remain nomina nuda. The status of each is discussed to avoid additional nomenclatural errors and continued taxonomic confusion.

Márquez & Asiain (2010) described three new species of the Philonthus furvus species group: P. navarretei and P. pollens from Mexico, and P. rufotibialis from Mexico and Guatemala. They also provided new state and locality records for P. hoegei, P. testaceipennis and P. yaqui, as well as a key for the identification of the species. In this work (Márquez & Asiain 2010) the depositories of the type material and material examined were indicated, except for the holotype of P. navarretei. Based on article 16 (names published after 1999) of the International Code of Zoological Nomenclature (International Commission on Zoological Nomenclature 1999), which indicates that species names must be accompanied by the explicit fixation of a holotype (16.4.1), a statement of intent that this will be deposited in a collection and a statement indicating the name and location of that collection (16.4.2), the species name is considered as an "unavailable name". Navarrete-Heredia & Newton (2013) placed P. navarretei Márquez & Asiain, 2010 as a nomen nudum because the term "nomen nudum" is often used loosely for names that do not meet one or more of the conditions necessary for availability in the International Code of Zoological Nomenclature.

Virus taxonomy: one step forward, two steps back.

In the July issue of Journal of Paleontology, 84(4), Sánchez (2010) proposed the new genus nameEmiliodontafor the Ordovician bivalve genusEmilianiaSánchez, 1999 because of assumed homonymy withEmilianiaHay and Mohler, 1967 (in Hay et al., 1967). The supposed senior name, the genusEmilianiaHay and Mohler, belongs to the coccolithophores, a group of unicellular eukaryotic algae, which have traditionally been treated as plants (e.g., Glaessner, 1945; Tappan, 1980; see also Green and Jordan, 1994; Andersen, 2004 for modern classification) and to which the International Code of Botanical Nomenclature (ICBN) applies. In the original description ofEmilianiaHay and Molher the ICBN was used (Hay et al., 1967, p. 447) and the name was validly published under its rules. Animals such as the bivalveEmilianiaSánchez, 1999, in contrast, are treated under the International Code for Zoological Nomenclature (ICZN). Both codes are independent (ICBN, Principle I: Greuter et al., 1993, 2000; McNeill et al., 2006; ICZN Article 1: Ride et al., 1985, 1999), and therefore the same names (“homonyms” sensu lato) can coexist under different codes. Consequently,EmilianiaSánchez andEmilianiaHay and Molher are not homonyms in a taxonomic sense but are both legitimate names under the respective code. Furthermore, the nameEmiliodontaSánchez 2010 is superfluous and illegitimate, as “[…] the name of an animal taxon is not to be rejected merely because it is identical with the name of a taxon that is not animal.” (ICZN Article 1.4: Ride et al., 1999).

The United States Food and Drug Administration (FDA) has recently adopted DNA barcoding for the purpose of determining the species identity of commercial seafood products. This effort has revealed instances of incongruence between current scientifically accepted taxon names and those utilized by the seafood industry in product labelling. One such case is that of “Portunushaanii”, a name utilized by the seafood industry to label commercial products under the market name “red swimming crab.” However, carcinologists currently regard P.haanii as synonym of Portunusgladiator Fabricius, 1798, which itself is the subject of debate over whether it is a secondary homonym of Cancer gladiator Fabricius, 1793. Further complicating matters, DNA barcode sequences from commercial products match GenBank sequences identified as Portunuspseudoargentatus Stephenson, 1961. Here the complicated taxonomic history of the Portunusgladiator complex is reviewed and a resolution proposed based on combined morphological descriptions and molecular phylogenetic analyses. It is demonstrated that, given the provisions of the International Code of Zoological Nomenclature and the current elevation of Monomia Gistel, 1848, to full genus rank, its type species, Portunusgladiator Fabricius, 1798, should be treated as a valid and available taxon name. It is also shown, upon examination and comparison of types and topotypic material that Monomiahaanii (Stimpson, 1858) is a distinct taxon from M.gladiator, and Portunuspseudoargentatus Stephenson, 1961, is a junior subjective synonym of M.haanii (Stimpson, 1858). Furthermore, it is shown that crab meat sold in the US currently labeled as “Portunushaanii” and/or “red swimming crab” is in fact M.haanii using comparative analysis of DNA barcode sequences between museum-vouchered reference specimens, whole crabs provided directly by a seafood importer, and processed commercial products purchased at retail.

THE International Commission on Zoological Nomenclature announces its intention of publishing at an early date a revised and up-to-date edition (1) of the "International Code of Zoological Nomenclature" and (2) of the "Official List of Generic Names in Zoology". The last edition of the English text of "The International Code of Zoological Nomenclature" was published some years before the War and is now out of date for various reasons, including the adoption by the International Congress of Zoology of changes in some of the Articles in the International Code. The revised edition will consist of the substantive French text (on left-hand pages) and the English translation (on right-hand pages). The volume, which will be fully indexed, will also contain a detailed analysis of all the "Opinions" so far rendered by the International Commission in regard to the interpretation of the provisions of the Code. "The Official List of Generic Names in Zoology" was established by the International Congress of Zoology at its meeting at Monaco in 1913 for the purpose of recording full particulars relating to the names of the 5,000–10,000 best known and most important genera in the animal kingdom with their type species. So far, however, only about seven hundred names have been placed on the "Official List", due largely to the fact that the decisions taken by the International Commission have never hitherto been brought together in a single volume and with a full index. It is hoped that the "Official List" will now develop into a powerful instrument for stabilizing zoological nomenclature. It is hoped that its publication in book form will stimulate specialists to make proposals for the addition of other generic names important not only in systematic zoology but also in the applied sciences and in the teaching of zoology at the universities.

Naming taxa from cladograms: A cautionary tale

Is Myxomycetes (Amoebozoa) a Truly Ambiregnal Group? A Major Issue in Protist Nomenclature

Taxon names are at the core of communication related to biodiversity. Thus, systems that regulate such names should prevent unnecessary changes. Unfortunately, the current regulatory codes have some articles that produce confusion or, even, generate name instability. To promote nomenclatural stability, while maintaining a system that effectively conveys information about biological diversity and its evolution, we argue in favor of emendations to the current International Code of Zoological Nomenclature (ICZN). We propose that taxon names should be created within an evolutionary framework; ideally, this would mean including a phylogenetic tree or, at the very least, formulating a hypothesis in words based on explicit arguments (homologous traits) for the evolutionary relatedness of taxa, avoiding subjective perceptions. Additionally, we consider that some relatively minor changes of the ICZN would greatly increase name stability; the most relevant modifications that would facilitate long-term stability are: (i) immutability of the species epithet of species names, (ii) intercalation of unranked taxa between formal Linnaean ranks, (iii) elimination of homonyms in taxon names at the genus-group level, and (iv) inclusion of flexible phylogenetic definitions when supraspecific taxa are named.