Nomenclature over 5 years in TaxonWorks: Approach, implementation, limitations and outcomes

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).

BackgroundIn order to designate the various concepts of taxa in biology, evolution and paleontology, scientists have developed various rules on how to create unique names for taxa. Different Codes of Nomenclature have been developed for animals, plants, fungi, bacteria etc., with standard sets of Rules that govern the formation, publication and application of the nomina of extant and extinct species. These Codes are the result of decades of discussions, workshops, publications and revisions. The structure and complexity of these Codes have been criticized many times by zoologists. This project aims, using the International Code of Zoological Nomenclature as a case study, to show that the structure of these Codes is better reflected and understood as networks.MethodsThe majority of the text of the Code has been divided into hundreds of Nodes of different types, connected to each other with different types of Edges to form a network. The various mathematical descriptors of the entire system, as well as for the elements of the network, have been conceptually framed to help describing and understanding the Code as a network.ResultsThe network of the Code comprises 1,379 Nodes, which are connected with 11,276 Edges. The structure of the Code can be accurately described as a network, a mathematical structure that is better suited than any kind of linear text publication to reflect its structure.DiscussionThinking of the Code as a network allows a better, in-depth understanding of the Code itself, as the user can navigate in a more efficient way, as well as to depict and analyze all the implied connections between the various parts of the Code that are not visible immediately. The network of the Code is an open access tool that could also help teaching, using and disseminating the Code. More importantly, this network is a powerful tool that allows identifying a priori the parts of the Code that could be potentially affected by upcoming amendment and revisions. This kind of analysis is not limited to nomenclature, as it could be applied to other fields that use complex textbooks with long editing history, such as Law, Medicine and Linguistics.

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.

The island of Madagascar is a renowned hotspot for adaptive radiations. Madagascar has been separated from mainland Africa since the end of the Jurassic, and from India since the Late Cretaceous. This long isolation, combined with the island’s large size and relatively few dispersal events has resulted in an avifauna characterized by a low species count and high endemism: for instance, 80% of the breeding Malagasy songbirds (Passeriformes) are endemic (Hawkins & Goodman 2003). A first series of papers (Cibois et al. 1999, 2001; Fjeldsa et al. 1999) on the phylogeny of the Malagasy taxa traditionally classified as Timaliidae, Sylviidae and Pycnonotidae (all families included in the large sylvioid clade) showed that several of these passerines form an original radiation endemic to the island. Because these results were based solely on a single kind of molecular marker (mitochondrial DNA sequences), the authors refrained at that time from giving a name to this clade. More recently, other studies using nuclear markers as well (Beresford et al. 2005; Johansson et al. 2008a, 2008b) confirm the existence of this Malagasy sylvioid radiation. The species that comprise this group exhibit a great variety of bill shapes, wing and tail proportions, and tarsus lengths. This diversity in morphology is linked to varieties of habitat and prey favoured by these insectivorous forest dwellers (Schulenberg 2003). Thus the endemic Malagasy sylvioid clade rivals other island radiations, including the vangas of Madagascar and the finches of the Galapagos, in ecological and morphological diversity. Several authors were inclined to consider this group at the family level, using the name ‘Bernieridae’. To our knowledge the first study using this name was the book “The natural history of Madagascar”, edited by S. M. Goodman and J. Benstead in 2003, where the name ‘Bernieridae’ appeared in two chapters (in Tingle et al. (2003: p. 522) and Hawkins & Goodman (2003: p. 1036), although Schulenberg (2003: p. 1131) referred to the Malagasy "warblers" in his chapter on the radiations of passerine birds on Madagascar). An alternative spelling for the family-group name, ‘Bernieriidae’, can be found in several personal pages on the internet, but we have not found an occurrence of this in any publication, as defined in the International Code of Zoological Nomenclature (4th edition, 1999). The name ‘Bernieridae’ was later used in several journal articles (Chouteau & Fenosoa 2008; Fuchs et al. 2008; Johansson et al. 2008a, 2008b), however, none of these have introduced the family-group name ‘Bernieridae’ according to the provisions of the International Code of Zoological Nomenclature, i.e. the nominal taxon was not explicitly indicated as intentionally new (Article 16.1) and the type genus was not cited (Article 16.2). In the present paper, we therefore propose to rectify this situation by correctly introducing the family-group name for the Malagasy sylvioid radiation.

Constraints in naming parts of the Tree of Life

Innovative electronic publication in plant systematics: PhytoKeys and the changes to the “Botanical Code” accepted at the XVIII International Botanical Congress in Melbourne

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.

Corrigendum to “Assessing phylogenetic dependence of morphological traits using co-inertia prior to investigate character evolution in Loricariinae catfishes” Mol. Phylogenet. Evol. 46 (2008) 986–1002

Family-group names proposed for beetles belonging to the family Cerambycidae are catalogued and their availability is determined using the rules of the current International Code of Zoological Nomenclature. A synoptic classification of the family summarizes the validity of the names. Type genera of all family-group names are listed and the type species and stems of genera of available family-group names are included. A new family-group name, Elytracanthinini Bousquet (type genus: Elytracanthina Monn, 2005, a replacement name for Elytracantha Lane, 1955) is proposed for Elytracanthinae Lane, 1955. Ichthyosoma armatum Montrouzier, 1855 is designated as type species of Icthyosoma Boisduval, 1835. Reversal of precedence is used to preserve the validity of the following family-group names: Anaglyptides Lacordaire, 1868 (over Anaglyptisidae Gistel, 1848 [Buprestidae]); Dryobiini Arnett, 1962 (over Dryobiadae Gistel, 1856 [Ptinidae]); Hemilophitae Thomson, 1868 (over Amphionychitae Thomson, 1860) and Hétéropsides Lacordaire, 1869 (over Dichophyiaeidae Gistel, 1848). The following family-group names, although junior synonyms, are preserved as valid until an application is submitted to the International Commission on Zoological Nomenclature; in these cases a reversal of precedence could not be applied: Eurypodini Gahan, 1906 (over Zaracinae Pascoe, 1869); Macronides Lacordaire, 1868 (over Enchapteritae Thomson, 1861); Pyresthides Lacordaire, 1868 (over Pseudolepturitae Thomson, 1861 and Erythrinae Pascoe, 1866) and Stenoderinae Pascoe, 1867 (over Syllitae Thomson, 1864). A total of 238 valid cerambycid family-group names (413 available names) are recognized in the following 13 subfamilies: Vesperinae (1 valid family-group name), Oxypeltinae (1), Disteniinae (4), Anoplodermatinae (3), Philinae (1), Parandrinae (2), Prioninae (24), Spondylidinae (5), Necydalinae (1), Lepturinae (8), Lamiinae (80), Dorcasominae (1), and Cerambycinae (107).

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.

The family-group names of animals (superfamily, family, subfamily, supertribe, tribe and subtribe) are regulated by the International Code of Zoological Nomenclature. Particularly, the family names are very important, because they are among the most widely used of all technical animal names. A uniform name and spelling are essential for the location of information. To facilitate this, a list of family-group names for fossil fishes has been compiled. I use the concept ‘Fishes’ in the usual sense, i.e., starting with the Agnatha up to the †Osteolepidiformes. All the family-group names proposed for fossil fishes found to date are listed, together with their author(s) and year of publication. The main goal of the list is to contribute to the usage of the correct family-group names for fossil fishes with a uniform spelling and to list the author(s) and date of those names. No valid family-group name description could be located for the following family-group names currently in usage: †Brindabellaspidae, †Diabolepididae, †Dorsetichthyidae, †Erichalcidae, †Holodipteridae, †Kentuckiidae, †Lepidaspididae, †Loganelliidae and †Pituriaspididae.

The family-group names of animals (superfamily, family, subfamily, supertribe, tribe and subtribe) are regulated by the International Code of Zoological Nomenclature. Family names are particularly important because they are among the most widely used of all technical animal names. Apart from using the correct family-group name according to the Code, it is also important to use one unique universal name (with a fixed spelling) to avoid confusion. We have compiled a list of family-group names for Recent fishes, applied the rules of the Code and, if possible, tried to conserve the names in prevailing recent practice. We list all of the family-group names found to date for Recent fishes (N=2625), together with their author(s) and year of publication. This list can be used in assigning the correct family-group name to a genus or a group of genera. With this publication we contribute to the usage of correct, universal family-group names in the classification of, and for communication about, Recent fishes.

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

Article 79 of the Fourth Edition of the International Code of Zoological Nomenclature (henceforth Code) describes an official List of Available Names in Zoology (henceforth LAN), consisting of a series of “Parts” (of defined taxonomic and temporal scope), compiled by relevant experts. The LAN represents a comprehensive inventory of names available under the Code. The aim of this manual is to define a procedure for implementing Article 79, with format suggestions for zoologists aiming to create a Part of the LAN for family-group, genus-group, or species-group names in zoological nomenclature. Because the LAN may serve as an important basis for retrospective content in ZooBank, the structure outlined here is designed to allow easy importation to ZooBank. A Part ultimately adopted for the LAN will contain nomenclaturally available names but not necessarily all those within the scope of the Part: the comprehensiveness of the candidate Part is at the discretion of the experts proposing the Part. They may choose to include all nomenclaturally available names or use the proposal of a Part to pare away nomina dubia so they lose “status in zoological nomenclature despite any previous availability” (to quote Articles 10.7 and 79.4.3; that this was the intention of the framers of Article 79 is clear from the Preface to the Code). Nonetheless, we advocate that the proposing body include an inventory of all known names deemed to be available so it will be obvious that names not advocated for inclusion in the Part have not simply been overlooked. Because a candidate Part of the LAN is for an entire taxon at the specified rank and for the specified period, it must include the names of both living and fossil representatives of the taxon. In the proposal for adding a Part to the LAN, an unavailable name corresponding to a later available one should be included in the Remarks section of the available name. Unavailable names that have not subsequently been made available can be added at the end of the candidate Part, along with information explaining them. The Commission and reviewers of the candidate Part will thereby have a list of such names and an understanding of why they are not available. Moreover, these names can be discussed during the periods required by Article 79 for input by the zoological community, when change in their status can be advocated by members of the community interested in the taxon under consideration.