Nomenclatural Issues Research Articles

Diversity and Taxonomy of Chrysophytes from the Pasvik State Nature Reserve (Russia)

Pasvik State Nature Reserve is situated in the Arctic zone and its chrysophyte flora is poorly studied. The diversity of the golden-brown algae (chrysophytes) from the Paz river, as well as the peat-bog on its bank, has been investigated using light and scanning electron microscopy. Overall, 34 chrysophyte taxa have been recorded. They represent fifteen genera from five orders. A new species of Synura, S. skaloudiorum, has been described. Morphologically, it resembles S. hibernica, a species restricted in its distribution to Ireland and Newfoundland, but differs mainly in size and structure of the apical scales. Nomenclatural issues on the selected chrysophyte taxa are discussed. The name Kephyrion starmachii was invalidly published, and it was validated. The new nomenclatural combination Chrysothecopsis tubulosus has been proposed. Also, Dinobryon sertularia var. annulatum Shi and Wei has been synonymized with D. annulatum Hilliard and Asmund.

The nomenclatural status of “Anoplophallus maculatus” Cope, 1895, its consequences on the systematics of Lycodon subcinctus auctorum, and the description of a new species (Squamata: Colubridae)

The Malayan banded wolf snake, Lycodon subcinctus (F. Boie, 1827) has a complicated taxonomic and nomenclatural history. For almost a century, the combination Anoplophallus maculatus Cope, 1895 has been applied to populations of L. subcinctus from southern China, with various authors recognizing the taxon maculatus as a subspecies (i.e., Lycodon subcinctus maculatus) or junior synonym. A recent study that proposed the elevation of Chinese L. subcinctus to species rank (as Lycodon “maculatus”) prompted us to re-investigate several nomenclatural issues relevant to Anoplophallus maculatus that have not been fully addressed in the literature. We show that Anoplophallus maculatus was not described as a new species, and actually refers to Megalops maculatus Hallowell, 1861, a Neotropical snake currently known as Leptodeira maculata (Dipsadinae). As a consequence, populations of L. subcinctus recently recognized as Lycodon “maculatus”, have no valid binomen applied to them. To resolve this issue, we provide a new species name for populations of L. subcinctus from China and include a morphological description based on specimens collected across all of mainland Southeast Asia. The new species, Lycodon neomaculatus sp. nov., occurs well outside of southern China, and inhabits Indochina (Cambodia, Laos, Thailand, Vietnam) and eastern Myanmar. Lycodon neomaculatus sp. nov. is distinguished from both L. sealei and L. subcinctus by subtle differences in adult dorsal color pattern and body scalation. The distributions of L. neomaculatus sp. nov. and L. subcinctus sensu stricto appear to be allopatric, and the Isthmus of Kra region in peninsular Thailand may act as a biogeographic filter separating the two species.

Untangling Zebrafish Genetic Annotation: Addressing Complexities and Nomenclature Issues in Orthologous Evaluation of TCOF1 and NOLC1.

Treacher Collins syndrome (TCS) is a genetic disorder affecting facial development, primarily caused by mutations in the TCOF1 gene. TCOF1, along with NOLC1, play important roles in ribosomal RNA transcription and processing. Previously, a zebrafish model of TCS successfully recapitulated the main characteristics of the syndrome by knocking down the expression of a gene on chromosome 13 (coding for Uniprot ID B8JIY2), which was identified as the TCOF1 orthologue. However, database updates renamed this gene as nolc1 and the zebrafish database (ZFIN) identified a different gene on chromosome 14 as the TCOF1 orthologue (coding for Uniprot ID E7F9D9). NOLC1 and TCOF1 are large proteins with unstructured regions and repetitive sequences that complicate alignments and comparisons. Also, the additional whole genome duplication of teleosts sets further difficulty. In this study, we present evidence that endorses that NOLC1 and TCOF1 are paralogs, and that the zebrafish gene on chromosome 14 is a low-complexity LisH domain-containing factor that displays homology to NOLC1 but lacks essential sequence features to accomplish TCOF1 nucleolar functions. Our analysis also supports the idea that zebrafish, as has been suggested for other non-tetrapod vertebrates, lack the TCOF1 gene that is associated with tripartite nucleolus. Using BLAST searches in a group of teleost genomes, we identified fish-specific sequences similar to E7F9D9 zebrafish protein. We propose naming them "LisH-containing Low Complexity Proteins" (LLCP). Interestingly, the gene on chromosome 13 (nolc1) displays the sequence features, developmental expression patterns, and phenotypic impact of depletion that are characteristic of TCOF1 functions. These findings suggest that in teleost fish, the nucleolar functions described for both NOLC1 and TCOF1 mediated by their repeated motifs, are carried out by a single gene, nolc1. Our study, which is mainly based on computational tools available as free web-based algorithms, could help to solve similar conflicts regarding gene orthology in zebrafish.

Taxonomic and Nomenclatural notes on Biophytum madurense, B. intermedium and B. intermedium var. pulneyense (Oxalidaceae) from South India

While revising the family Oxalidaceae for the Western Ghats (SW India), missing typification and nomenclatural issues about several species of Biophytum were noticed. In this contribution, Biophytum intermedium var. pulneyense is reduced to a synonym of B. madurense and neotypes for the names B. madurense and B. intermedium are designated. A brief description, photographs, and taxonomic note on these species are provided to facilitate their identification.

Taxonomic notes and nomenclatural corrections in Crustacea: Isopoda (exclusive of Oniscidea)

During a review of all isopod taxa (exclusive of Oniscidea), nomenclatural and taxonomic issues were found that need correction or detailed explanation. Herein, details are provided on five unreplaced species/subspecies homonyms, corrections to authorship and/or date for six genera, two families/subfamilies and 11 species, three unavailable names for subfamilies, 22 corrections to the spelling of specific names to conform to the gender of their respective genera, two junior homonyms that are replaced, and one genus that is validated herein. The history of Ianthe Bovallius, 1881 and its numerous replacement names, Brongniartia Eights, 1833, and Ceratoserolis Brandt, 1988 are discussed, a type species is selected for Vireia Viré, 1903, and Epicepon is validated as a genus name.

On the genus Flabellamon Ng, 1996, with descriptions of two new species (Crustacea: Brachyura: Potamidae)

The history, taxonomy and nomenclatural issues revolving around the genus Flabellamon Ng, 1996, are reviewed. The genus of late contained two species, F. kuehnelti (Pretzmann, 1963) and F. wanchaii Takeda, Sanpool & Intapan, 2019. In the process of this review, two new species of this genus were uncovered from historical materials that were previously misidentified, and described herein as, F. ngankee sp. nov. (from northwestern Thailand) and F. mulayit sp. nov. (from southeastern Myanmar). Flabellamon ngankee sp. nov. is most similar superficially to F. wanchaii but can be distinguished easily by morphological differences in carapace armature, external orbital tooth, male pleonal margins and male gonopod. Flabellamon mulayit sp. nov. on the other hand, is more similar morphologically to F. kuehnelti, but can also be distinguished easily by epibranchial tooth and male gonopod characters. An identification key to the species of Flabellamon is provided.

Prorocentrum canariense sp. nov., a case of pseudo-cryptic speciation in the cosmopolitan dinoflagellate P. compressum (Prorocentrales, Dinophyceae).

The planktonic dinoflagellate Prorocentrum compressum is widespread in warm and temperate seas. A strain identified as P. cf. compressum BEA 0681B isolated from the island of Gran Canaria, NE Atlantic Ocean, showed a divergence in rDNA/ITS phylogenies with respect to P. compressum. The Canarian strain was oval, with an average length-to-width ratio of 1.35, smooth thecal surface with less than 150 thecal pores, including oblique pores, sometimes with a bifurcated opening. In contrast, P. compressum was rounder, with a length-to-width ratio < 1.2, with reticulate-foveate ornamentation and 200-300 pores per valve. We propose Prorocentrum canariense sp. nov. These species clustered as the most early-branching lineage in the clade Prorocentrum sensu stricto. Although this clade mainly contains planktonic species, the closer relatives were the benthic species P. tsawwassenense and P. elegans. Interestingly, P. compressum and P. canariense sp. nov. are widely distributed in temperate and warm seas without an apparent morphological adaptation to planktonic life. The formation of two concentric hyaline mucilaginous walls could contribute to this success. We discuss the use of Prorocentrum bidens to solve the nomenclature issue of P. compressum that was described citing a diatom as basionym.

Notes on the taxonomy of the species complex Symphytum tuberosum (Boraginaceae) and on the interpretation of the name S. microcalix

The name Symphytum microcalix originally published by P.M. Opiz is currently interpreted in two different ways, namely as a synonym of Symphytum officinale or as a name of a taxon from the S. tuberosum aggregate. The application of the name is discussed based on the analysis of Opiz’s protologue, with notes on the origin of the authentic material, and on the spelling of the name. It is concluded that Opiz’s description was most likely based on an anomalous plant of Symphytum bohemicum and thus it is not applicable to any representatives of the S. tuberosum aggregate. Further nomenclatural and taxonomic issues within the S. tuberosum aggr. are discussed, with a special emphasis on the status of Ukrainian representatives of this species complex.

Typifications in Pavonia Cav. sect. Lopimia (Malvaceae)

ABSTRACT Pavonia is represented by 270 species concentrated in South America. Among these representatives, names grouped in the subgenus Pavonia exhibited nomenclatural and typification problems, especially within the section Lopimia. The nomenclatural issues discussed in this work were observed during the taxonomic revision process of Pavonia section Lopimia. In this context, the aim of this study was to correctly associate names with their respective types and indicate lectotypes and neotypes when necessary. This study presents two neotypifications and 10 lectotypifications.

Alyxia Banks ex R.Br. in New Caledonia: a clarification of several species complexes, nomenclatural notes, and a description of three new species

The genus Alyxia Banks ex R.Br. is partially revised for New Caledonia, with 31 species recognised. The species complex Alyxia tisserantii Montrouz. is discussed and divided into seven species with existing names, and the synonymy is updated accordingly. Alyxia loeseneriana var. macrocarpa Boiteau is elevated to species status due to new flowering material with the name A. paniensis Lannuzel nom. nov., stat. nov. created to accommodate it, due to the preexisting Alyxia macrocarpa Koord. Detailed study of Alyxia caletioides (Baill.) Guillaumin ex Däniker revealed it was in fact made up of two distinct taxa; a new separate species, Alyxia urceolata Lannuzel, sp.nov. is therefore described. Two new species are also described following their recent collection: Alyxia humboldtensis Lannuzel &amp; Gâteblé, sp.nov. is restricted to the summit of Mount Humboldt, and Alyxia minimiflora Lannuzel, sp.nov. is known from schistaceous cliffs around Nouméa. Finally, several nomenclatural issues are discussed, and an updated key to the genus in New Caledonia is provided.

Changes in the terminology and diagnostic criteria of non-alcoholic fatty liver disease: Implications and opportunities.

Fatty liver disease (FLD) is a highly prevalent pathological liver disorder. It has many and varied etiologies and has heterogeneous clinical course and outcome. Its proper nomenclature and classification have been problematic since its initial recognition. Traditionally, it was divided into two main categories: Alcohol-associated liver disease and nonalcoholic FLD (NAFLD). Among these, the latter condition has been plagued with nomenclature and classification issues. The two main objections to its use have been the use of negative (non-alcoholic) and stigmatizing (fatty) terms in its nomenclature. Numerous attempts were made to address these issues but none achieved universal acceptance. Just recently, NAFLD has received a new nomenclature from an international collaborative effort based on a rigorous scientific methodology. FLD has been renamed steatotic liver disease (SLD), and NAFLD as metabolic dysfunction-associated SLD. Metabolic dysfunction-associated steatohepatitis was chosen as the replacement terminology for non-alcoholic steatohepatitis. This is a significant positive change in the nomenclature and categorization of FLD and will likely have a major impact on research, diagnosis, treatment, and prognosis of the disease in the future.

Tetrahedrite-(Cu), Cu12Sb4S13, from Bankov near Košice, Slovak Republic: a new member of the tetrahedrite group

AbstractTetrahedrite-(Cu), Cu12Sb4S13, has been approved as a new mineral species (IMA2022–078) from the Bankov magnesite deposit near Košice, Slovak Republic where it occurs as anhedral grains, up to 0.4 mm across, associated with skinnerite, chalcostibite, famatinite, tetrahedrite-(Fe) and zoned aggregates of tennantite-(Cu) to tennantite-(Fe). Tetrahedrite-(Cu) is steel-grey, with a metallic lustre. Mohs hardness is ca. 3½–4 and calculated density is 5.029 g.cm–3. In reflected light, tetrahedrite-(Cu) is isotropic and grey with a bluish shade. Reflectance data for the four COM wavelengths in air are [λ (nm): R (%)]: 470: 31.1; 546: 30.1; 589: 29.9; and 650: 28.1. The empirical formula, based on electron-microprobe data (mean of 17 spot analyses), is Cu11.42Zn0.26Fe0.19(Sb4.06As0.08)Σ4.14S12.99. The ideal formula is Cu6(Cu4Cu2)Sb4S13, which requires (in wt.%) Cu 45.76, Sb 29.23 and S 25.01, total 100.00. Tetrahedrite-(Cu) is cubic, I$\bar{4}$3m, with unit-cell parameters a = 10.3296(15) Å, V = 1102.2(5) Å3 and Z = 2. Its crystal structure was refined by single-crystal X-ray diffraction data to a final R1 = 0.0347 on the basis of 261 unique reflections with Fo &gt; 4σ(Fo) and 22 refined parameters. Tetrahedrite-(Cu) is isotypic with other tetrahedrite-group minerals. Previous findings of tetrahedrite-(Cu) are reported and some nomenclature issues, related to the Fe and Cu oxidation states, are discussed. At the Bankov deposit, tetrahedrite-(Cu) is related to hydrothermal, most probably Alpine, solutions strongly enriched in Cu, Sb and S.

Meeting Necessity instead of Serendipity: Miscellaneous Nomenclatural Notes on Asteraceae

While compiling a continuously updated checklist of families and genera of world embryophytes, the authors find it necessary to resolve some nomenclatural issues in Asteraceae (Compositae). Here we propose a new supertribal classification for Asteroideae with five supertribes, two of which (Calendulodae and Anthemidodae) are new and one (Ambrosiodae) is a replacement name. A new tribe Leucomerideae in Stifftioideae is described, with the monotypic Nouelia newly treated as a synonym. Two older generic names, Anacis and Epilepis, are resurrected to follow the revision of Coreopsis s.l. and to avoid later homonymy or superfluity, alongside with necessary new combinations. A new nothogenus ×Coreacis is thereby established. The correct spelling Malacotrichinae of the subtribe ‘Malacothricinae’ is discussed.

A new atlas to study embryonic cell types in Xenopus

This paper introduces a single-cell atlas for pivotal developmental stages in Xenopus, encompassing gastrulation, neurulation, and early tailbud. Notably surpassing its predecessors, the new atlas enhances gene mapping, read counts, and gene/cell type nomenclature. Leveraging the latest Xenopus tropicalis genome version, alongside advanced alignment pipelines and machine learning for cell type assignment, this release maintains consistency with previous cell type annotations while rectifying nomenclature issues. Employing an unbiased approach for cell type assignment proves especially apt for embryonic contexts, given the considerable number of non-terminally differentiated cell types. An alternative cell type attribution here adopts a fuzzy, non-deterministic stance, capturing the transient nature of early embryo progenitor cells by presenting an ensemble of types in superposition. The value of the new resource is emphasized through numerous examples, with a focus on previously unexplored germ cell populations where we uncover novel transcription onset features. Offering interactive exploration via a user-friendly web portal and facilitating complete data downloads, this atlas serves as a comprehensive and accessible reference.

Catalog of Anaedus Blanchard, 1842 with nomenclatural notes (Coleoptera: Tenebrionidae: Lagriinae)

The genus Anaedus Blanchard, 1842 in the tribe Goniaderini Lacordaire, 1859 has experienced drastic genus-level change where seven other genera were subsumed as synonyms by Aalbu et al. (2023). That study addressed multiple nomenclatural issues including several replacement names, but did not provide a full species-group catalog. This study presents a full catalog for the 142 species-group names currently belonging to Anaedus and rectifies several nomenclatural issues missed within the previous study. The catalog includes full nomenclatural histories and type localities for all taxa. The following New Combinations are established: Anaedus keralensis (Kaszab, 1979), An. madrensis (Kaszab, 1979), An. philippinus (Schawaller, 1994), An. setosus (Kaszab, 1979), An. simillimus (Kaszab, 1979). The following New Replacement Names are established for the species listed in parentheses: Anaedus fairmairei Kanda &amp; Johnston (replaces An. fulvipennis Fairmaire, 1889), An. pici Kanda &amp; Johnston (replaces An. rufipes Pic, 192), An. pictus Kanda &amp; Johnston (replaces Spinolyprops maculatus Kulzer, 1954), An. neorufescens Kanda &amp; Johnston (replaces Aspisoma rufescens Pic, 1951).

Wagler vs. Fitzinger: Leposternon microcephalus, a fight over gender (Sauria, Amphisbaenidae)

This short note provides some insight into an academic “battle” between early 19th century herpetologists about a small but interesting nomenclatural issue, namely the grammatically correct gender of a species epithet. Most texts used in the current note (Wagler in Spix 1824; Fitzinger 1826a‒b; Schlegel 1826; Wagler 1827) were published in 19th century German, which sometimes made use of vocabulary that is no longer employed nowadays. The old German texts are translated here into English in a way that they reflect modern language as much as possible.

Translating nanoEHS data using EPA NaKnowBase and the resource description framework.

The U.S. Federal Government has supported the generation of extensive amounts of nanomaterials and related nano Environmental Health and Safety (nanoEHS) data, there is a need to make these data available to stakeholders. With recent efforts, a need for improved interoperability, translation, and sustainability of Federal nanoEHS data in the United States has been realized. The NaKnowBase (NKB) is a relational database containing experimental results generated by the EPA Office of Research and Development (ORD) regarding the actions of engineered nanomaterials on environmental and biological systems. Through the interaction of the National Nanotechnology Initiative's Nanotechnology Environmental Health Implications (NEHI) Working Group, and the Database and Informatics Interest Group (DIIG), a U.S. Federal nanoEHS Consortium has been formed. The primary goal of this consortium is to establish a "common language" for nanoEHS data that aligns with FAIR data standards. A second goal is to overcome nomenclature issues inherent to nanomaterials data, ultimately allowing data sharing and interoperability across the diverse U.S. Federal nanoEHS data compendium, but also in keeping a level of consistency that will allow interoperability with U.S. and European partners. The most recent version of the EPA NaKnowBase (NKB) has been implemented for semantic integration. Computational code has been developed to use each NKB record as input, modify and filter table data, and subsequently output each modified record to a Research Description Framework (RDF). To improve the accuracy and efficiency of this process the EPA has created the OntoSearcher tool. This tool partially automates the ontology mapping process, thereby reducing onerous manual curation. Here we describe the efforts of the US EPA in promoting FAIR data standards for Federal nanoEHS data through semantic integration, as well as in the development of NAMs (computational tools) to facilitate these improvements for nanoEHS data at the Federal partner level.

Nomenclatural updates in the sedge-flora of western Uttar Pradesh

Establishing all plant’s correct identity and nomenclature is crucial in the current context. Therefore, an updated list and nomenclature status of sedges of western Uttar Pradesh, India has been provided in this article. This research paper incorporates extensive consultation of taxonomic databases, examination of type specimens and scrutiny of published works, including Ph.D thesis, research papers, books, and floras. To ensure the accuracy of binomial nomenclature, a systematic approach is adopted, starting with the utilization of search engines to cross-verify and validate taxonomic information. This includes a rigorous examination of online databases and repositories to access up-to-date information on botanical nomenclature. This paper aims to provideaccepted binomials with correct author citations of the sedges growing in western Uttar Pradesh because several names in the published literature are not accepted now. Such publications include several synonyms as accepted name, as well as mistakes in authority. A pivotal aspect of this work involves the verification of binomial identities through the examination of protologues and type specimens. Keeping this in mind, a comprehensive study for solving and updating nomenclature issues hasbeen carried out using different databases, websites and recent publications. We updated the nomenclature of all sedges of western Uttar Pradesh included in publications after 1959. Review of literature and field studies shows that western Uttar Pradesh includes a total of 91 species belonging to 14 genera published in 18 publications. In this study, 25 names of past publications were corrected. This is the first report on updated name changes in the floristic component of western Uttar Pradesh, where 41 names of sedges have been updated. This research paper covers the accepted name, synonym, taxonomic treatment, and typification.

Current Understandings and Open Hypotheses on Extracellular Circular RNAs.

Circular RNAs (circRNAs) are closed RNA loops present in humans and other organisms. Various circRNAs have an essential role in diseases, including cancer. Cells can release circRNAs into the extracellular space of adjacent biofluids and can be present in extracellular vesicles. Due to their circular nature, extracellular circRNAs (excircRNAs) are more stable than their linear counterparts and are abundant in many biofluids, such as blood plasma and urine. circRNAs' link with disease suggests their extracellular counterparts have high biomarker potential. However, circRNAs and the extracellular space are challenging research domains, as they consist of complex biological systems plagued with nomenclature issues and a wide variety of protocols with different advantages and disadvantages. Here, we summarize what is known about excircRNAs, the current challenges in the field, and what is needed to improve extracellular circRNA research.

Contribution to the knowledge of Gongolaria barbata (Sargassaceae, Fucales) from the Mediterranean: insights into infraspecific diversity

Gongolaria barbata (Sargassaceae, Fucales) is a widespread species for which several infraspecific taxa have been described, indicating its polymorphism. This study contributes to the understanding of the molecular, nomenclatural, morphological and ecological aspects of G. barbata in the Mediterranean and sheds light on the infraspecific diversity and its implications for the taxonomy of this species. Molecular analyses were performed using sequencing of the mitochondrial cox1 gene on both haptophytic and pleustophytic forms from different sites in the Adriatic and Tyrrhenian Seas. Vegetative and reproductive morphology was studied on thalli samples from the Adriatic. Our results showed that there are different morphotypes within G. barbata populations related to specific environmental conditions, suggesting infraspecific variation. In contrast, molecular analyses showed no differences between samples, regardless of whether individuals are growing “attached” to a substrate or “unattached”. We also discussed the taxonomic status and nomenclatural issues related to certain infraspecific taxa previously proposed for G. barbata. In particular, the confusion surrounding Cystoseira aurantia is clarified.