Code Of Nomenclature Research Articles

Roholtiella volcanica sp. nov., a New Species of Cyanobacteria from Kamchatkan Volcanic Soils

During a study of biodiversity of cyanobacteria in Gorely volcano soils (Kamchatka Peninsula), a strain of heterocytous, a false branching cyanobacterium with gradually tapered filaments, was isolated. Prominent features of the strain were purplish-grey trichomes and firm, distinct multilayered sheaths. Based on the results obtained from the morphological, ecological, and phylogenetic analysis using the 16S rRNA and 16S–23S ITS region, 16S–23S ITS secondary structure analysis, comparison of flanking regions of BoxB and V3 helices, and the p-distance between the 16S–23S ITS region, we describe our strain K7 as a novel species of the genus Roholtiella with the name Roholtiella volcanica sp. nov., in accordance with the International Code of Nomenclature for algae, fungi, and plants. This work continues the rapid expansion of the description of new taxa of cyanobacteria, and particularly demonstrates a coming phase in cyanobacterial taxonomy in which the discovery of new species in recently described genera rapidly increases our understanding of the diversity in this phylum.

Lectotypification of <i>Dendrobium heyneanum</i> Lindl. (Orchidaceae)

Dendrobium heyneanum Lindl. is lectotypified in accordance with the International Code of Nomenclature (ICN).

PhycoBank: Repository for algal novelties

The International Code of Nomenclature (ICN) for algae, fungi, and plants calls for indexing of names in nomenclatural repositories (Turland 2018, Art. 42). Scientific names, new combinations, validations, and typifications of algae are novelties tracked by PhycoBank, the registration system for algae. PhycoBank was established and institutionalized at the Botanic Garden Berlin as the repository for nomenclatural acts concerning algae. Since June 2018, PhycoBank staff have been operating the registration system permanently. All data entered into the system undergo a curatorial process to assure a high level of data quality. PhycoBank’s three main components comprise a user-friendly data entry web application available for all registered submitters (self-registration allowed) and curators, a public data access portal, and a search engine that integrates most of the larger online repositories for algae names. The latter is not only a prerequisite for reliable data curation during the registration process but also a valuable, publicly available online tool for algae names. A fourth component still under development is handling the tight integration of the registration system with the workflow of digital publishers. The resulting data are expected to be of high quality and to have been intensively checked against existing nomenclatural acts worldwide. A crucial requirement for the data entry application is thus an intensive support for data validation and curation. Besides the search index giving access to a huge number of existing external names, the data entry application offers a set of tools for quality assurance. It supports and requires the creation of mostly fully atomized data that strictly follow the rules of the ICN. Additionally, completeness for core data is mandatory. Both, atomization and completeness are a precondition to achieve the required uniqueness in the dataset. Completeness also implies that new combinations can only be registered after or together with their original name. The same applies to bi- or trinomials and the respective uni- and binomials they are built on. The publicly available data portal allows accessing published registrations by searching for scientific names, nomenclatural authors, higher ranks and for each part of a bibliographic reference (such as bibliographic author, journal, title, year) stored in PhycoBank. Being a name centric application PhycoBank is neutral with respect to taxonomic opinions. Therefore, only nomenclatural synonymies (basionym or replaced synonym relationships) are stored in the system and names are not attached to a unique classification. Instead, to facilitate search via higher ranks as required by users, classification information is stored as a directed graph of higher taxa with registered names linking to this graph. By this, searches can be performed on multiple classifications simultaneously and can return all possible matches. PhycoBank uses http-based persistent identifiers (e.g. http://phycobank.org/102170), which makes them resolvable and actionable. These identifiers link to nomenclatural acts only and not to the information in the act. That is, a PhycoBank identifier should not be used to refer to a scientific name even if this name was established in the nomenclatural act. PhycoBank makes use of the application stack offered by the EDIT Platform for Cybertaxonomy (Kohlbecker 2017). However, as registration workflows essentially differ from other taxonomic workflows, a completely new user interface for editing has been developed, which provides the users with an intuitive and fluent user experience despite the high complexity of the data. The Common Data Model (Müller 2017) is the core data model for the Platform and already covered the vast majority of data types and fields required by the registration in terms of completeness and degree of atomization. For PhycoBank, it only needed to be extended by a single data type representing the registration/nomenclatural act itself. As of July 2022, PhycoBank includes 4,332 registrations, of which 4,202 are name novelties (1,523 in preparation or ready, 239 under curation, 2,407 published, and 33 rejected); 130 registrations refer to lectotypes or epitypes of existing names. PhycoBank will apply for recognition as a repository in 2022. This is a prerequisite for a proposal to make registration of nomenclatural acts for algae mandatory. This is possible before, at or after the 20th International Botanical Congress 2024.

Chrysanthemumdabieshanense, a new name for Chrysanthemumvestitum var. latifolium (Asteraceae, Anthemideae).

Recent phylogenetic analyses have revealed that Chrysanthemumvestitumvar.latifolium and C.vestitumvar.vestitum were placed in different clades based on their chloroplast genomes and nuclear LFAFY gene sequences. Accordingly, based on previous morphological analysis, molecular phylogenetic results, fieldwork, and herbarium studies, Chrysanthemumvestitumvar.latifolium should be raised to the species level. Considering the condition of the material found and Articles 6.9, 6.11, 41.2, 58.1 of the International Code of Nomenclature for Algae, Fungi, and Plants (Shenzhen Code) that is currently in force, Chrysanthemumdabieshanense Z.X.Fu, A.G.Zhen, & Y.P.Ma, nom. nov. is proposed as the new name for Chrysanthemumvestitumvar.latifolium J.Zhou & Jun Y.Chen. The detailed emended description, distribution map, insights into its habitat, and an updated comparative morphological study are presented in this study.

Nomenclatural solutions for diagnosing ‘cryptic’ species using molecular and morphological data facilitate a taxonomic revision of the Black-bellied Salamanders (Urodela, Desmognathus ‘quadramaculatus’) from the southern Appalachian Mountains

To be available under the International Code of Zoological Nomenclature, nomina erected after 1930 must “be accompanied by a description or definition that states in words characters that are purported to differentiate the taxon” (Article 13.1.1). For many so-called ‘cryptic’ species, this may prove difficult when relying on external morphology. Yet, such species are likely to be diagnosable by (fixed or variable) differences in DNA sequences, which can also be treated as characters and described in words. While recent authors have proposed such methods, they have rarely been adopted as the primary diagnostic implement in vertebrates. Additionally, morphometrics may reveal subtle but distinct variation in size and shape, which may not be dispositive for identifying individual specimens but can nonetheless characterize overall differences between species. We employ these techniques here to revise the taxonomy of the Black-bellied Salamanders Desmognathus folkertsi and Desmognathus ‘quadramaculatus’ from the southern Appalachian Mountains of the eastern United States. While the former was diagnosed by a variety of morphological and molecular characters, the latter was poorly characterized and subsequently found to consist of two distantly related clades of six genetic lineages. Recent nomenclatural work found that the nomen Salamandra quadramaculata Holbrook, 1840 was unavailable for this species and that no valid nomen had ever been applied at the species level. We erect three new species and resurrect one junior synonym to account for species-level geographic genetic variation in the group. All nomina are diagnosed with explicit reference to fixed or varying allelic differences at mitochondrial and nuclear loci, quantitative variation in overall size and shape from linear morphometrics, and qualitative description of color-pattern variation. Despite their gross similarity, we hypothesize that subtle, as-yet undetected phenotypic variation exists between these species, which may be revealed by geometric morphometrics, 3D scanning, and other data such as physiology and behavior. We also utilize recently developed technologies to present DNA-sequence data for these species in a compact, reproducible format to permanently associate the observed characters with the original description, with several thousand base pairs taking up only a few cm2. These approaches may prove useful for future descriptions of amphibians with highly similar external phenotypes.

The nomenclatural case of Holopyga italica Dahlbom, 1845 and Colpopyga flavipes (Eversmann, 1858) (Hymenoptera, Chrysididae)

The case of the forgotten name Holopyga italica Dahlbom, 1845 and its currently used, junior subjective synonym Hedychrum flavipes Eversmann, 1858 (currently Colpopyga flavipes) is discussed. Since H. italica has been listed as a valid species after 1899, in the world catalogue by Kimsey & Bohart (1991), the reversal of precedence cannot be automatically applied to this case. However, provisions of the International Code of Zoological Nomenclature argue for the conservation of the name Hedychrum flavipes against that of Holopyga italica. The case will be referred to the International Commission on Zoological Nomenclature, for a ruling under its Plenary Power, and meanwhile the use of the junior synonym H. flavipes is to be maintained.

Proposal (29) to conserve the name Omphalodo nitidae-Coryletum avellanae Amigo, G. Azcárate et Romero 1994 with a conserved type

The association Omphalodo nitidae-Coryletum avellanae was defined by assembling relevés on (mainly) Corylus avellana woods on nutrient-rich substrates in the westernmost part of the Cantabrian Range (NW Spain). However, a mesophytic oak forest dominated by Quercus robur (with noteworthy amount of Corylus avellana in the undercanopy) was selected as its holotype. The most common interpretation of this association in the subsequent literature has been as seral Corylus avellana forests. For this reason, we propose the application of article 53 of the ICPN (4th ed.), which allows the name to be maintained with a new nomenclatural type based on the more recent interpretation of this syntaxon. (29) Omphalodo nitidae-Coryletum avellanae Amigo, G. Azcárate et Romero 1994, typus cons. propos. Typus: Amigo et al. (1994), table 2: rel. 4 (typus cons. propos.) Taxonomic reference: Castroviejo et al. (1986–2020). Syntaxonomic reference: Rivas-Martínez (2011). Abbreviations: ICPN = International Code of Phytosociological Nomenclature.

On the edge of the Shivaliks: An insight into the origin and taxonomic position of Pakistani toads from the Duttaphrynus melanostictus complex (Amphibia, Bufonidae)

The common Asian toad Duttaphrynus melanostictus (Schneider, 1799) complex has a wide distribution ranging from western foothills of the Himalaya to the easternmost range of the Wallacea, with the evidence of human-mediated introductions to some other areas. In the entire distribution range, the complex is formed by several evolutionary clades, distributed mostly in South-East Asia with unresolved taxonomy. In the northwestern edge of its distribution (Pakistan), the name D. melanostictus hazarensis (Khan, 2001) has been assigned to local populations but its biological basis remained, so far, understudied and unvalidated. Therefore, we re-evaluated the available genetic data (mitochondrial and nuclear) to show the relationships between Pakistani populations (including the type locality of D. m. hazarensis) and others from across the range. Our results showed that Pakistani populations are associated with one, deeply diverged, well-supported and widely distributed clade (so-called Duttaphrynus sp. 1 according to 16S, or clade B based on tRNAGly-ND3), that has already been detected in previous studies. This clade is further distributed in India, Nepal, Bangladesh, Malaysia, Singapore, and Indonesia and is characterized by a low level of genetic variability. This further suggests that both natural, as well as potential human-mediated dispersal, might have played an important role in setting up the current phylogeographic and distribution pattern of this clade. The clade is deeply divergent from other clades of the complex and represents a taxonomically unresolved entity. We here argue that the clade Duttaphrynus sp. 1/B represents a distinct species for which the name Duttaphrynus bengalensis (Daudin, 1802) comb. nov. is applicable, while the description of D. m. hazarensis does not satisfy the rules of the International Code of Zoological Nomenclature.

More discussion of minimalist species descriptions and clarifying some misconceptions contained in Meier et al. 2021.

This is a response to a preprint version of "A re-analysis of the data in Sharkey et al.'s (2021) minimalist revision reveals that BINs do not deserve names, but BOLD Systems needs a stronger commitment to open science", https://www.biorxiv.org/content/10.1101/2021.04.28.441626v2. Meier et al. strongly criticized Sharkey et al.'s publication in which 403 new species were deliberately minimally described, based primarily on COI barcode sequence data. Here we respond to these criticisms. The following points are made: 1) Sharkey et al. did not equate BINs with species, as demonstrated in several examples in which multiple species were found to be in single BINs. 2) We reiterate that BINs were used as a preliminary sorting tool, just as preliminary morphological identification commonly sorts specimens based on color and size into unit trays; despite BINs and species concepts matching well over 90% of species, this matching does not equate to equality. 3) Consensus barcodes were used only to provide a diagnosis to conform to the rules of the International Code of Zoological Nomenclature just as consensus morphological diagnoses are. The barcode of a holotype is definitive and simply part of its cellular morphology. 4) Minimalist revisions will facilitate and accelerate future taxonomic research, not hinder it. 5) We refute the claim that the BOLD sequences of Plesiocoelusvanachterbergi are pseudogenes and demonstrate that they simply represent a frameshift mutation. 6) We reassert our observation that morphological evidence alone is insufficient to recognize species within species-rich higher taxa and that its usefulness lies in character states that are congruent with molecular data. 7) We show that in the cases in which COI barcodes code for the same amino acids in different putative species, data from morphology, host specificity, and other ecological traits reaffirm their utility as indicators of genetically distinct lineages.

Healthcare use at the end of life of patients with congenital heart disease: does heart failure matter?

Abstract Funding Acknowledgements Type of funding sources: Foundation. Main funding source(s): Research Foundation Flanders (to PM, EG, and LVB) European Society of Cardiology (Nursing Training Grant to LVB) Background Heart failure (HF) is a common cause of morbidity and mortality in patients with congenital heart disease (CHD). Although limited in scope, previous studies suggest that patients with heart failure follow a specific end-of-life trajectory with episodes of serious complications, which may impact the patterns of care as death approaches. Aims The study aims to identify differences in characteristics and patterns of care in the last year of life in deceased CHD patients with and without HF. Methods This retrospective study used data of deceased adult patients included in the BELgian COngenital heart disease Database combining Administrative and Clinical data (BELCODAC). To describe patterns of care in the last year of life, we captured information about hospitalisations, emergency department visits, and visits to the general practitioner using nomenclature codes. Heart failure was identified as having HF as cause of death and/or at least one prescription of a loop diuretic in the last year of life. Sensitivity analyses with a stricter definition for HF (HF as cause of death or ≥ 1 prescription of a loop diuretic combined with a prescription of digoxin, dopamine, dobutamine, other non-glycoside stimulants, metoprolol, bisoprolol, carvedilol, aldosterone antagonists, ACE inhibitors or ARBs) were performed as well. Results During the period 2007–2016, 390 adults with CHD died, of which 170 patients with HF (44%). Patients with HF were older, died more often due to a cardiovascular cause of death, and had more complex heart lesions, compared to patients without HF (Table 1). While the number of emergency department visits and hospitalisations in the last year was similar, patients with HF had almost twice as much monthly visits at the general practitioner in their last year of life (Table 1). As shown in Figure 1, the mean number of hospitalisations and emergency department visits increased in a similar fashion throughout the last year of life, but the pattern of general practitioner visits was substantially different for patients with and without HF. The sensitivity analyses, in which a stricter definition for HF was used, yield very similar results. In these analyses, the difference in mean monthly hospitalisations was also significant between the two groups. Conclusions This study shows clinically important differences in characteristics and patterns of care of deceased patients with CHD with and without heart failure. Patients with HFhave different needs and should receive a tailored approach at the end of life. Future research is needed to understand these differences and investigate these patients' end-of-life care needs in more detail. Funding acknowledgments: This work was supported by Research Foundation Flanders; European Society of Cardiology; the King Baudouin Foundation; the National Foundation on Research in Pediatric Cardiology; and the Swedish Research Council for Health, Working Life and Welfare-FORTE.

Clarification of the status of Paraferreola Šustera, 1912 as an available genus name in Pompilidae, and the identity of Sphex ursus Fabricius, 1793 in Mutillidae (Hymenoptera)

The usage of Paraferreola Šustera, 1912 since its proposal as a genus of spider wasps, but based on a misidentified type species (Sphex ursus Fabricius, 1793, actually a species of Mutillidae), shows that it continues to be applied (although infrequently) in Pompilidae, despite the proposal of new names (Eoferreola Arnold, 1935 and Tea Pate, 1946) for the equivalent generic concept. Application of Article 70.3.2 of the fourth edition of the International Code of Zoological Nomenclature permits correction of the erroneous type species designation to that originally intended (Sphex rhombica Christ, 1791), and thus the maintenance of Paraferreola as a valid genus in Pompilidae. Examination of the holotype specimen of Sphex ursus has shown it to be a senior synonym of Mutilla vesta Cresson, 1865 and its junior synonyms, for which the valid name must thus be Dasymutilla ursus (Fabricius, 1793), comb. nov.

The naming of Homo bodoensis by Roksandic and colleagues does not resolve issues surrounding Middle Pleistocene human evolution.

Roksandic et al. (2022) proposed the new species name Homo bodoensis as a replacement name for Homo rhodesiensis Woodward, 1921, because they felt it was poorly and variably defined and was linked to sociopolitical baggage. However, the International Code of Zoological Nomenclature includes regulations on how and when such name changes are allowed, and Roksandic et al.'s arguments meet none of these requirements. It is not permitted to change a name solely because of variable (or erroneous) later use once it has been originally defined correctly, nor can a name be modified because it is offensive to one or more authors or to be politically expedient. We discuss past usage of H. rhodesiensis and the relevant nomenclatural procedures, the proposed evolutionary position of H. bodoensis, and issues raised about decolonizing paleoanthropology. We reject H. bodoensis as a junior synonym, with no value from its inception.

Description of Desmonostoc caucasicum sp. nov. (Cyanobacteria) using an integrative taxonomic approach

ABSTRACT A new cyanobacterial species of the genus Desmonostoc is described according to the International Code of Nomenclature for algae, fungi, and plants. The new species Desmonostoc caucasicum sp. nov. is recorded in the mountain meadow subalpine soil from the Greater Caucasus, Russia. The analysis is based on morphological characters, the 16S rRNA gene phylogenetic analysis, and ITS secondary structure. Desmonostoc caucasicum differs from the other species of the genus in colony morphology, size of vegetative cells and heterocytes, and habitat type. The 16S rRNA gene sequence of the new strain displayed 95.3%–97.9% similarities to other species of the genus Desmonostoc. The phylogeny inferred by maximum likelihood and Bayesian inference placed D. caucasicum in the Desmonostoc clade, within the Nostocaceae. The novel strain formed an independent lineage within the clade. The D1–D1ʹ, Box–B and V3 helices obtained from the 16S–23S ITS region didn’t fit those of any described species of Desmonostoc. Amplification of a fragment of the mcy gene involved in microcystin biosynthesis from D. caucasicum confirmed that it has this genetic determinant. An integrative taxonomic approach, based on morphological, 16S rRNA and mcy genes molecular analyses, ITS secondary structure, along with ecological data, is used to delimit this new species.

A potential intellectual property issue with the way in which some nomenclature code decisions are made

AbstractThis article examines the legal status of nomenclature codes and their application to denomination in certain forms of intellectual property, in particular plant breeder's rights and patents for micro‐organisms. Its objective is to show how rigidity and the absence of appeals against nomenclature decisions can have adverse effects on the rights and even earning potential of applicants.

Towards a unified taxonomic catalogue for the Chilean cacti: assembling molecular systematics and classical taxonomy

The competition between floristic catalogues and the nomenclatural issues of the treated taxa, is a problem for the botanical knowledge of countries. Consequently, it seems to be necessary to merge former taxonomical proposals into a unified list based on phylogenetic hypotheses, the rules of nomenclature and dichotomous keys to the Chilean subfamilies, tribes and genera. With this approach we here propose an updated catalogue of the Chilean cacti. It would be necessary to merge the various taxonomic proposals into a unified list based on both phylogenetic hypotheses and the rules of nomenclature. With this approach, we here propose to updated the catalogue of Chilean cactus. A neotype was designated for Echinocactus jussieui. In addition, we present a dichotomous taxonomic key to the Chilean subfamilies, tribes, and genera.

Effective typification of Avena pubescens (Poaceae; Pooideae)

Avena pubescens Hudson was previously considered to have been “neotypified” by Röser in 1995 from a specimen preserved at WU herbarium (Wien). However, there is an original element that was included and cited in the protologue. Therefore, the typification by Röser is here briefly discussed and superseded because is being contrary to Art. 9.8 of the International code of nomenclature for algae, fungi, and plants (Shenzhen Code). The name is lectotypified in this paper with an illustration published by Ray in 1724. In addition, for a precise circumscription of the name, an epitype is proposed from a complete and well preserved specimen at WU.

Teaching organic nomenclature for pharmacy students: Adapting a course to online mode during COVID-19

Introduction: Due to the confinement of the COVID-19 pandemic, educational centres have remained closed, transferring the teaching process to online mode, thus adapting infrastructure, methodologies, and the university community. Objectives: This work aims to evaluate the effectiveness of strategies in learning organic nomenclature and seek student opinions about committing fraud in organic chemistry course assessments in the online mode in the pharmaceutical career. Methods: The methodologies used allowed the students to understand and apply the organic nomenclature rules, using online collaborative guides and crosswords worked in synchronous classes, previous reading, and the collaborative asynchronous creation of informative files for the recognition of heterocyclic compounds and formative assessment. All assessments were applied in three-people groups in the synchronous classes. Finally, an anonymous survey was administered to know the student perception of the possibility of fraud during the course. Results: A substantial improvement (from 47.7% to 80.5%) was observed in the application of IUPAC rules for organic compounds. Of the students who responded to the anonymous survey, 81% reported that the methodology used decreased the opportunity to commit fraud during assessments.

Chaenomeles japonica (Maleae, Amygdaloideae, Rosaceae): validation of six Alberts Tīcs’ cultivar names and two new synonyms for the species

Chaenomeles is a rosaceous genus of Asian origin with eight species, including four artificially created hybrids. Several species of this genus are used in many countries for ornamental plants and fruit production. As a result of many years of breeding work in Latvia, Alberts Tīcs selected six Chaenomeles japonica (Japanese quince) cultivars. Unfortunately, when publishing the descriptions of his cultivars, he does not comply with the requirements of the International Code of Nomenclature for cultivated plants because the names of newly introduced cultivars are not validly published. In his publications on the cultivation of Chaenomeles, Tīcs has introduced new scientific names, which have been published without complying with the requirements of the International Code of Nomenclature for algae, fungi, and plants. The validation of Tīcs’ cultivar names has been performed here, and the names—Chaenomeles maulei f. pomifera-inermis nom. nud. and Chaenomeles ×pomoidea nom. nud.—have been recognized as new synonyms of Chaenomeles japonica. Descriptions have been provided for all Alberts Tīcs’ cultivars.

Harmonizing Prokaryotic Nomenclature: Fixing the Fuss over Phylum Name Flipping.

ABSTRACTLloyd and Tahon recently criticized proposed bacterial phylum nomenclature changes (K.G. Lloyd, G. Tahon, Nat Rev Microbiol 20:123-124, 2022, https://doi.org/10.1038/s41579-022-00684-2) precipitated by the International Committee on Systematics of Prokaryotes (ICSP)’s official recognition of phylum nomenclature rules. Here, we extend the critique. While we applaud bringing consistency to phylum names, we prognosticate what this minute but momentous change entails for the future of microbial nomenclature and how this will sow confusion among researchers. Several pitfalls of the proposed ICSP framework-based nomenclature are also detailed, including (i) improper type genus name and suffix usage, (ii) loss of Bacteria/Archaea distinctions, (iii) disruption of major phylum name prefixes, and (iv) absence of organism name prevalidation. Finally, we suggest new names for the key bacterial phyla Proteobacteria (Proteobacteriota), Firmicutes (Firmicuteota), Actinobacteria (Actinobacteriota), and Tenericutes (Tenericuteota), while keeping the archaeal phylum names Crenarchaeota, Thaumarchaeota, and Euryarchaeota. Together, these changes will help researchers attain chaos-free uniform nomenclature.

Astroblastocystis nom. nov. - a new replacement name for Blastocystis Jaekel, 1918 (Echinodermata, Parablastoidea).

The generic name Blastocystis has been proposed at least twice for different organisms for which nomenclature is governed by the International Code of Zoological Nomenclature. Blastocystis Jaekel, 1918, is a junior homonym of the generic name Blastocystis Alexeieff, 1911. We propose the following Astroblastocystis nom. nov. as a new replacement name (neonym) for Blastocystis Jaekel, 1918.