On the unavailability of five reptilian names

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

This Editorial provides advice on how to upload information to ZooBank for manuscripts that include new taxonomic names. This is a requirement of the International Code of Zoological Nomenclature, to ensure that new taxonomic names are accepted as valid in electronic publication of manuscripts prior to print publication. Hence, the Journal of Fish Biology requires that the procedure outlined below is followed for any new taxonomic names. Amendment of Article 8 of the International Code of Zoological Nomenclature to expand and refine methods of publication (Bulletin of Zoological Nomenclature 2012 69, 161–169) requires that: Article 8.5. To be considered published, a work issued and distributed electronically must be registered in the Official Register of Zoological Nomenclature (ZooBank) and contain evidence in the work itself that such registration has occurred. Accordingly, the Journal of Fish Biology requires that any manuscript dealing with the description of new species, genera or families, submitted to the journal, must be registered in ZooBank and the name of each new taxonomic name (e.g. new family, genus or species) should be added to ZooBank. urn:lsid:zoobank.org:act:XXXXXXXX-XXXXX-XXX-XXXX-XXXXXXXXXXXX (a series of numbers and letters). urn:lsid:zoobank.org:pub:XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX (a series of numbers and letters). Note the identification numbers for publications include ‘pub’ in the sequence number. The ZooBank identification number for the manuscript must be included in your manuscript on the title page of your manuscript submitted to the Journal of Fish Biology, following the author names and affiliations for your manuscript. The ZooBank identification number for each new species should appear at the start of the definition of the new taxon, as below: Aus bus, new species urn:lsid:zoobank.org:act:XXXXXXXX-XXXXX-XXX-XXXX-XXXXXXXXXXXX Figure 1; Tables I & II (While the International Code of Zoological Nomenclature does not require the species register numbers to be included in the electronic publication, the Journal of Fish Biology requests this information, to conform with protocols of several other taxonomic journals.) Once your manuscript has been published electronically, please ensure to update the status of your ZooBank record for the manuscript from ‘not yet published’ to ‘published.’ This will then ensure the name is publicly searchable in the ZooBank database. ZooBank has tutorial videos on all steps of the process (creating an account; registering a publication; then registering the new names in that publication): http://zoobank.org/VideoGuide/ We are grateful to C. Ferraris for bringing this information to our attention, and to M. DeJong (Cline Library, Northern Arizona University) for providing information about online archives that store the Journal of Fish Biology. I.J.H. is grateful to the American Museum of Natural History (Department of Ichthyology) for supporting Research Associate status.

Journal of Eukaryotic MicrobiologyVolume 65, Issue 2 p. 290-290 CorrigendumFree Access Corrigendum to ″Schmidingerothrix salinarum nov. spec. is the Molecular Sister of the Large Oxytrichid Clade (Ciliophora, Hypotricha) by Foissner et al. 2014″ This article corrects the following: Schmidingerothrix salinarum nov. spec. is the Molecular Sister of the Large Oxytrichid Clade (Ciliophora, Hypotricha) Wilhelm Foissner, Sabine Filker, Thorsten Stoeck, Volume 61Issue 1Journal of Eukaryotic Microbiology pages: 61-74 First Published online: December 10, 2013 First published: 20 November 2017 https://doi.org/10.1111/jeu.12481AboutSectionsPDF 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 onFacebookTwitterLinkedInRedditWechat In the article: Foissner, W., Filker, S., and Stoeck T. 2014. Schmidingerothrix salinarum nov. spec. is the Molecular Sister of the Large Oxytrichid Clade (Ciliophora, Hypotricha). J. Eukaryot. Microbiol., 61(1): 61–74. https://doi.org/10.1111/jeu.12087, the ZooBank registration number was omitted. Foissner et al. (2014) described the morphology, ontogeny, and phylogeny of a new Schmidingerothrix species in this electronic-only journal. Since the electronic article does not contain ZooBank registration, it is not published (available) with respect to the International Code of Zoological Nomenclature (ICZN 1999, 2012, Articles 8.5, 9.11). However, such work likely remains available as source for further purposes, similar to a suppressed work (ICZN 1999, Article 8.7.1). To become available, Schmidingerothrix salinarum must be registered in ZooBank (ICZN 2012). ZooBank registration http://zoobank.org/urn:lsid:zoobank.org:pub:33751519-8DAB-42CD-814E-C72926D5E39F Schmidingerothrix salinarum nov. spec. (Table 2 and Fig. 1A–L, 2A–M, 3A–D, 4A–H, 5, 6A–F, 7A–I, 8A–D in Foissner et al. 2014) Diagnosis (from Foissner et al. 2014, p. 73). Size in vivo about 95 × 17 μm. Body slender (~5.5:1), usually widest in mid-portion, with short but distinct tail. Four macronuclear nodules, forming a series near right margin of cell; zero to two micronuclei. Cortical granules in loose rows, colorless, about 1 μm across. Three frontal cirri and three frontoventral cirral rows. Frontal cirrus 1 subapical close to ventral part of adoral zone of membranelles. Frontoventral row 1 composed of an average of four cirri; row 2 of 18 cirri; row 3 of five cirri. Right marginal row composed of an average of 23 cirri, left of 17. Adoral zone about 32% of body length, composed of an average of three frontal and 21 ventral membranelles. Endoral membrane 12 μm long on average. Type locality. Solar saltern in the Ria Formosa National Park near to the town of Faro, Portugal, W7°57′41.0684″, N37°00′29.4851″. Type material. The holotype slide and two paratype slides with protargol-impregnated specimens and two paratype slides with hematoxylin-stained cells have been deposited in the Biologiezentrum of the Oberösterreichische Landesmuseum in Linz (LI), Austria, reg. no. 2013/33–37. Relevant specimens have been marked by black ink circles on the coverslip. Etymology. See same section in Foissner et al. (2014, p. 74). Morphology of Schmidingerothrix salinarum nov. spec. See same section in Foissner et al. (2014, p. 63, Table 2, and Fig. 1A–L, 2A–M, 3A–D, 4A–H). Molecular phylogeny. See same section in Foissner et al. (2014). GenBank accession number. KC991098 (SSU rDNA; length 1,769 bp; GC content 45.11%). Ontogenesis of Schmidingerothrix salinarum nov. spec. See same section in Foissner et al. (2014, p. 67 and Fig. 6A–F, 7A–H, 8A–D). Discussion. For comparison of Schmidingerothrix salinarum Foissner et al., 2017 with S. extraordinaria Foissner, 2012, type of the genus, see same section in Foissner et al. (2014, p. 72). Remarks: In future, this species has to be cited as “Schmidingerothrix salinarum Foissner, Filker & Stoeck, 2017” (for justification, see introduction). Literature Cited Foissner, W. 2012. Schmidingerothrix extraordinaria nov. gen., nov. spec., a secondarily oligomerized hypotrich (Ciliophora, Hypotricha, Schmidingerotrichidae nov. fam.) from hypersaline soils of Africa. Eur. J. Protistol., 48: 237– 251. Foissner, W., Filker, S. & Stoeck, T. 2014. Schmidingerothrix salinarum nov. spec. is the molecular sister of the large oxytrichid clade (Ciliophora, Hypotricha). J. Eukaryot. Microbiol., 61: 61– 74. ICZN (International Commission on Zoological Nomenclature) 1999. International Code of Zoological Nomenclature. International Trust for Zoological Nomenclature, London, 306 p. ICZN (International Commission of Zoological Nomenclature) 2012. Amendment of Articles 8, 9, 10, 21 and 78 of the International Code of Zoological Nomenclature to expand and refine methods of publication. Bull. Zool. Nom., 69: 161– 169. Volume65, Issue2March/April 2018Pages 290-290 ReferencesRelatedInformation

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.

Bibliography resembles some species complexes with such overlapping diversity that they can be regarded as a single polymorphic species or as an assemblage of several closely allied and subtly distinguishable species or as a hybrid swarm derived from intercrossing in past. It is a matter of definition. As John Carter has said in his ABC for Book-Collectors (1952), may be enumerative, analytical or descriptive; broadly defined, it is the description or knowledge of books in regard to their authors, subjects, editions and history. Thus in biological terms biblio­ graphy is a polymorphic species embracing numerous variants, i.e. lines of enquiry. Some of these, however, interest only bibliophiles. Others are highly relevant to procedures in natural history and have accordingly received much attention within Natural History Museum during past hundred years; moreover their utility will continue. The importance of bibliography for such an institution as Natural History Museum at South Kensington, which is primarily taxonomic in its research, comes from importance of printed record as a long-lasting continuously usable source of taxonomic information. For this information to be retrievable with minimum of inconvenience and loss of time, stability of nomenclature and resolving of synonymy are in turn important. As stated in International Code of Botanical Nomenclature, principle III, the nomenclature of a taxonomic group is based upon priority of publication. The International Code of Zoological Nomenclature puts same emphasis on priority: the valid name of a taxon is oldest available name applied to it... provided that name is not invalidated by any provision of this Code or has not been suppressed by Commission. Relative dates of publication of competing different names for same organism or of like names for different organisms can thus determine name which should be adopted. To ascertain relative dates of publication often involves difficult and time-consuming bibliographical enquiry but this must nevertheless be undertaken when result may be crucial for correct nomenclature. That is why Natural History Museum has long been a major centre of such bibliographical enquiry and why Society for Bibliography of Natural History was formed under Museum's auspices in 1936 and has received so much support from Museum. The Society has never been officially part of Museum, but this Museum support has been vital to its maintenance and success. On other hand Society, by publishing results of bibliographic al and associated biographical enquiry relevant to natural history, has much benefited workers in Museum and elsewhere. The relations of two, in biological terms, have not been simply commensal but symbiotic.

NOMENCLATURE OF CULTIVATED PLANTS: A HISTORICAL BOTANICAL STANDPOINT

International Code of Zoological Nomenclature Adopted by the XV International Congress of Zoology. Editorial Committee: N. R. Stoll (Chairman), R. Ph. Dollfus, J. Forest, N. D. Riley, C. W. Sabrosky, C. W. Wright and R. V. Melville (Secretary). Published for the International Commission on Zoological Nomenclature by the International Trust for Zoological Nomenclature, London. Pp. i-xvii + 1 + 176, 8 vo, cloth. Published [6 November] 1961. Obtainable from Int. Trust for Zool. Nomenclature, 19 Belgrave Square, London, S.W. 1, England. Price, $3.00 postpaid. Get access International Code of Zoological Nomenclature Adopted by the XV International Congress of Zoology. Editorial Committee: N. R. Stoll (Chairman), R. Ph. Dollfus, J. Forest, N. D. Riley, C. W. Sabrosky, C. W. Wright and R. V. Melville (Secretary). Published for the International Commission on Zoological Nomenclature by the International Trust for Zoological Nomenclature, London. Pp, i-xvii + 1 + 176, 8 vo, cloth. Published [6 November] 1961. Obtainable from Int. Trust for Zool. Nomenclature, 19 Belgrave Square, London, S.W. 1, England. Price, $3.00 postpaid. E. Raymond Hall E. Raymond Hall Search for other works by this author on: Oxford Academic Google Scholar Journal of Mammalogy, Volume 43, Issue 2, 29 May 1962, Pages 284–286, https://doi.org/10.2307/1377122 Published: 29 May 1962

Constraints in naming parts of the Tree of Life

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.

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.

Zoological nomenclature is the obligate medium by which we communicate taxonomic information, and a series of precise nomenclatural rules are designed to minimize confusion and ambiguity. The longest used, internationally applicable system of nomenclature is “Linnaean Nomenclature” (LN) (Polaszek & Wilson 2005), which has provided a stable platform capable of simultaneously designating discrete taxa and conveying their phylogenetic relationships, through the use of scientific names (nomina; Dubois 2000). Precise adherence to the rules of nomenclature as defined by the International Commission on Zoological Nomenclature (ICZN) is all the more important today when zoologists have millions of taxa to name. The recent importation of exogenous practices into LN is both confusing and inacceptable under the rules of the ICZN. Such practices include the use of a prefix Pan- in the family-series nomenclature. The nomenclature of all taxa from rank subspecies to superfamily is regulated by the International Code of Zoological Nomenclature (ICZN Code; Anonymous 1999). This means that all zoologists who endorse LN should use nomina complying with the rules of the ICZN Code for taxa of all ranks, including those from superfamily to subtribe and additional intermediate ranks of the nominal family group, also called family-series. However, some recent publications using LN do not follow the ICZN Code in several respects, concerning in particular (1) the rules of formation of nomina and (2) their authorship and date. Recent articles involving fossil birds (Smith 2011, 2013; Smith & Mayr 2013), explicitly or implicitly following the ICZN Code, illustrate both problems, representative of these recent practices. We wish to emphasize that our comments are in no way criticisms directed toward the core information of these studies, otherwise extremely useful, but rather a more general and formal invitation to follow more closely the ICZN Code. We found few other published examples of similar practice concerning birds (“Pan-Apodidae” in Mayr & Manegold 2002, also used by Ksepka et al. 2013; “Pan-Trochilidae” in Mayr & Manegold 2002 and Mayr 2007; “Pan-Hemiprocnidae” in Mayr & Manegold 2002; for articles published in a LN frame). We use hereafter the “Pan-Alcidae” example.

Several proposals have recently been published regarding the possible incorporation of nomenclature of higher taxa (class-series nomina) into the International Code of Zoological Nomenclature. Some basic questions related to this problem are discussed here. Introducing standard endings for the nomina of these taxa would probably be a kind of hara-kiri for LinnaeanStricklandian nomenclature of higher taxa: it would upset nomenclatural stability by introducing many new nomina and abandoning most of the nomina that have been in constant use in zoology for a long time to other nomenclatural systems alternative to the Code. Nomina of higher taxa should rather all belong in a single nominal-series, the class-series. They should not be submitted to a Rule of Coordination (except for identical taxa of different ranks), and their allocation to taxa should not be made through extensional or intensional definitions, but through ostension with a special system combining onomatophores (the conucleogenera) and onomatostases (the alienogenera). This system provides clear, unambiguous, stringent and universal Rules for the nomination of higher taxa in the future, compatible with all taxonomic systems including “phylogenetic” ones, while respecting the freedom of taxonomic thought and actions, as well as the tradition long attached to nomina of higher taxa in zoology.

The purpose of the International Code of Zoological Nomenclature (hereafter ‘the Code’) is to promote nomenclatural stability. If the Rules are changed every tenth year or so, Zoological Nomenclature will have to adapt each time to the new rules, which will be a source of instability. Another thing will be that the taxonomists will have to consider each time under which edition of the Code nomenclatural acts will have been done, which will unnecessarily complicate his work, and will even be a cause of mistakes. We do not think that a new Code is necessary, for the moment at least.

Based on a molecular phylogeny, a new phylogenetic taxonomy that is compatible with both the International Code of Zoological Nomenclature (ICZN) and the PhyloCode is proposed for Glassfrogs and their sister taxon, Allophryne ruthveni. The arrangement presented herein emphasizes the recognition of clades having (i) significant statistical support and congruence among phylogenetic estimation methods (i.e., parsimony, maximum likelihood, and Bayesian inference criteria), (ii) congruence among genetic markers, and (iii) morphological and/or behavioral distinctiveness. Also, when previously recognized groups are recovered as monophyletic or nearly monophyletic, we propose taxa that minimize the number of name changes required to make these groups monophyletic, preserving the names and contents of previous classifications (i.e., nomenclatural stability). The evolutionary proximity of Centrolenidae and Allophrynidae is recognized by combining these families into an unraked taxon, Allocentroleniae—a proposal that maintains the traditional names and species contents of Centrolenidae and Allophrynidae. We arrange centrolenid diversity in two subfamilies: Centroleninae and Hyalinobatrachinae. Within Centroleninae, the diagnosis and species content of the genera Centrolene, Cochranella, and Nymphargus are modified; Teratohyla is resurrected and modified, and Chimerella, Espadarana, Rulyrana, Sachatamia, and Vitreorana are proposed as new genera. The other subfamily, Hyalinobatrachinae, contains the new genus Celsiella and a modified Hyalinobatrachium that fully corresponds to the former fleischmanni Group. Additionally, the genus Ikakogi is described. Ikakogi could not be assigned with confidence to either subfamily and it is placed as incertae sedis in Centrolenidae. The data at hand suggest that Ikakogi tayrona is a lineage as old as the subfamilies Hyalinobatrachinae and Centroleninae. The revised taxonomy differs markedly from previous arrangements, which were based on phenetics and few morphological characters. Most of the genera defined herein are confined to distinct biogeographic regions, highlighting the importance of geography in the speciation of Glassfrogs. The principal limitation of this proposal is that it is based on an incomplete sampling of taxa (54% of the recognized Glassfrogs). Although diagnoses are based on phenotypic traits, there are several cases (16% of all species) in which the allocation of species is ambiguous because of morphological homoplasy and the lack of molecular data. Finally, in an attempt to facilitate species identification, comparison, and generic placement, we provide photographs for most (~ 96%) of the recognized centrolenid species.

To the Editor: Our 2002 article in Emerging Infectious Diseases about nomenclature changes for organisms in the genus Pneumocystis (1) has been widely cited and probably will remain a source for persons seeking information about this subject. Therefore, we need to correct an error in 1 of the species names presented in our article and in the 1999 article by Frenkel (2) on which our article was based. In the 1999 article, Frenkel proposed that the species of Pneumocystis found in humans be named to honor the Czech parasitologist, Otto Jirovec. The 1999 article was his second proposal for this change. In 1976, he first named the human pathogen Pneumocystis jiroveci (3), at which time it was classified as a protozoan and therefore named according to the International Code of Zoological Nomenclature. By 1999, it had become clear that the organisms in the genus Pneumocystis are fungi, which are named according to the International Code of Botanical Nomenclature (ICBN) (4). Differences between the International Code of Zoological Nomenclature and ICBN resulted in the realization of an error in the species epithet proposed by Frenkel in 1999, and our 2002 article contained this error. Frenkel’s 1999 article should have modified the species epithet from “jiroveci” to “jirovecii,” (ICBN Articles 32.7 and 60.11 and Rec. 60C.1b). The correct and valid name under ICBN is Pneumocystis jirovecii. Redhead et al. further explain the basis for this correction (5).