Botanical Nomenclature Research Articles

Toward the Madrid Code: nomenclatural proposals of Ukrainian botanists

The International Code of Nomenclature for algae, fungi, and plants is the document that regulates the nomenclature of taxa belonging to these groups of organisms, and thus it is crucially important for maintaining stability of scientific names applied to them. Stable, universal, and properly regulated nomenclature is a solid basis of biological taxonomy and all fields of science and other human activities depending on knowledge of living and fossil organisms. The Code is governed by the users represented by members of the Nomenclature Section of an International Botanical Congress. The Nomenclature Section has a power to modify the Code by voting and taking actions on formal proposals to amend the Code that are submitted by the users before the Congress. In this article, information is provided on the nomenclatural proposals by Ukrainian botanists (and one mycologist), or with participation of Ukrainian botanists, submitted to the XX International Botanical Congress (XX IBC) held in Madrid in July 2024. In total, nine Ukrainian scientists from Kyiv (M.G. Kholodny Institute of Botany of the National Academy of Sciences of Ukraine) and Lviv (Institute of Ecology of the Carpathians of the National Academy of Sciences of Ukraine, Ivan Franko National University of Lviv) have submitted 29 proposals to amend the Code, or 6.7% of the total number of proposals to amend the Code submitted to the XX IBC. These proposals were either single authored, or co-authored by Ukrainian authors and/or authors from other countries. Some of the accepted (3), accepted as amended (2), and rejected proposals are considered and briefly discussed. The participation and contribution of Ukrainian scientists in the process of amending the International Code of Nomenclature for algae, fungi, and plants are emphasized.

Description of Millerago gen. nov. based on taxogenomic analysis, with two new species, Millerago phaffii f.a., sp. nov. and Millerago galiae f.a., sp. nov.

Four yeast isolates obtained from tree bark and fermenting sap of Quercus spp. and insects in Colombia and Japan were phylogenetically related to Candida galis based on analyses of the sequences of the internal transcribed spacer (ITS) region and the D1/D2 domains of the large subunit rRNA gene. The novel species differs from C. galis by 20 nt substitutions and 5 indels in the D1/D2 sequences. A phylogenomic analysis suggested that these species are related to Candida ficus, the genus Phaffomyces and a small clade containing Barnettozyma botsteinii, Barnettozyma siamensis and Candida montana. Our genomic analyses suggest that the novel species and C. galis should be separated in a novel yeast genus. We propose the genus Millerago gen. nov. to accommodate these species and the species Millerago phaffii f.a., sp. nov. (CBS 18021T; MycoBank MB856172) to accommodate the Colombian and Japanese isolates. The Colombian isolate of M. phaffii differs from the Japanese isolates by three nt substitutions and one indel and two substitutions and one indel in the ITS and D1/D2 sequences, respectively, showing that they were conspecific. We also propose the new species Millerago galiae sp. nov. to validate this species according to the rules of the International Code of Nomenclature for algae, fungi and plants.

Botanists voted to remove offensive names; will zoologists follow?

The Nomenclature Section of the XX International Botanical Congress (IBC) was held from 15 to 19 July 2024, with 173 registered delegates in Madrid plus 219 additional attendees participating online (Gostel et al. 2014). It deliberated 433 proposals to amend the International Code of Nomenclature for algae, fungi, and plants (Turland et al. 2018, the Shenzhen Code). Among the decisions, one received significant media attention and was featured in top journals Science (Ortega & Stokstad 2024) and Nature (Callaway 2024): the removal of the letter c and the second f (if applicable) from 301 racially offensive names that include caf[e]r- and caff[e]r- (Smith & Figueiredo 2021). This proposal, along with others on offensive names (e.g., Hammer & Thiele 2021), received heated debates in Megataxa (Pethiyagoda 2023; Smith & Figueiredo 2023) and other journals (e.g., Jiménez-Mejías et al. 2024, with summaries of debates prior to this paper).

Two new species of Dulcicalothrix (Nostocales, Cyanobacteria) from India and erection of Brunnivagina gen. nov., with observations on the problem of using multiple ribosomal operons in cyanobacterial taxonomy.

Two new species of Dulcicalothrix, D. adhikaryi sp. nov. and D. iyengarii sp. nov., were discovered in India and are characterized and described in accordance with the rules of the International Code of Nomenclature for algae, fungi, and plants (ICN). As a result of phylogenetic analysis, Calothrix elsteri is reassigned to Brunnivagina gen. nov. During comparison with all Dulcicalothrix for which sequence data were available, we observed that the genus has six ribosomal operons in three orthologous types. Each of the three orthologs could be identified based upon indels occurring in the D1-D1' helix sequence in the ITS rRNA region between the 16S and 23S rRNA genes, and in these three types, there were operons containing ITS rRNA regions with and without tRNA genes. Examination of complete genomes in Dulcicalothrix revealed that, at least in the three strains for which complete genomes are available, there are five ribosomal operons, two with tRNA genes and three with no tRNA genes in the ITS rRNA region. Internal transcribed spacer rRNA regions have been consistently used to differentiate species, both on the basis of secondary structure and percent dissimilarity. Our findings call into question the use of ITS rRNA regions to differentiate species in the absence of efforts to obtain multiple operons of the ITS rRNA region through cloning or targeted PCR amplicons. The ITS rRNA region data for Dulcicalothrix is woefully incomplete, but we provide herein a means for dealing with incomplete data using the polyphasic approach to analyze diverse molecular character sets. Caution is urged in using ITS rRNA data, but a way forward through the complexity is also proposed.

Expanding the cyanobacterial flora of India: Multiple novel species of Nostoc and Desmonostoc from Jammu and Kashmir, India using a polyphasic approach.

This investigation reports the polyphasic characterization of six cyanobacterial strains that were isolated from Basantgarh village of district Udhampur in the union territory of Jammu and Kashmir, India. Morphological examination of the isolated strains indicated that the strains are members of the genus Nostoc or its morphotypes. Phylogenetic analyses using the 16S rRNA gene showed that five strains clustered in the Nostoc sensu stricto clade, whereas one strain clustered in the Desmonostoc clade. Further, comparative studies with their phylogenetically related taxa, based on morphology, folded secondary structures, phylogeny of the ITS rRNA region, and the percent genetic homology of 16S rRNA gene and ITS rRNA region clearly established the strains as novel taxa belonging to the genera Nostoc and Desmonostoc. Also, two strains 21A-PS and 2JNA-PS emerged as conspecific to each other, representing the same species of Nostoc. Hence, in accordance with the International code of Nomenclature for algae, fungi, and plants, this study describes Nostoc jammuense, Nostoc globosum, Nostoc breve, and Nostoc coriaceum, as novel species of the genus Nostoc, while Desmonostoc raii is described as a novel species of the genus Desmonostoc. This study adds novel species of Nostoc from Indian habitats and reinforces the need to explore the Nostoc sensu stricto clade for more novel taxa.

Nomenclatural standards of iris cultivars bred at the Peter the Great Botanical Garden of the V.L. Komarov Botanical Institute of RAS

Nomenclatural standards of five iris cultivars, namely ‘Andrey Kniazev’, ‘Eduard Regel’, ‘Marishka’, ‘Temuri’, and ‘Vitosha’ bred at the Peter the Great Botanical Garden of the V.L. Komarov Botanical Institute of RAS have been prepared in accordance with the rules and recommendations outlined in the International Code of Nomenclature for Cultivated Plants, and in the VIR methodological guidelines for the vegetatively propagated plants. Each nomenclatural standard is one herbarium sheet with all parts of a flowering plant accompanied by photos of flowers. Nomenclatural standards are registered in the VIR Herbarium database and deposited in the Herbarium of Cultivated Plants of the World, their Wild Relatives and Weeds (WIR) at the National Center for Plant Genetic Resources.

Nomenclatural standards and microsatellite profiles of raspberry cultivars bred at the I.V. Michurin Federal Scientific Center

Nomenclatural standards of three raspberry (Rubus idaeus L.) cultivars ‘Kleopatra’ (WIR-98480), ‘Sulamif’’ (WIR-98517) and ‘Shakhrazada’ (WIR-98536) bred at the I.V. Michurin Federal Scientific Center (FSC) were prepared according to the International Code of Nomenclature for Cultivated Plants. The nomenclatural standards of these cultivars have been transferred to N.I. Vavilov Federal Research Center of the All-Russian Institute of Plant Genetic Resources (VIR) for storage in the Herbarium of Cultivated Plants of the World, Their Wild Relatives and Weeds (WIR). Plant material for herbarium specimens was collected in the experimental field of the I.V. Michurin FSC by the cultivars’ author and handed to VIR for genotyping as well as for preservation in the live collection of VIR in compliance with the comprehensive strategy for registering and preserving domestic cultivars of the vegetatively propagated crops in a genebank. Microsatellite profiles of the three cultivars in question were obtained by using six nuclear SSR-markers. The genotyped specimens of the same raspberry cultivars, genotypically identical to the nomenclatural standards, were transferred to the VIR field collection and preservation in controlled conditions in the VIR in vitro collection.

Correction of collection number errors in the protologues of twenty-three names of Chinese vascular plants

Examination and collation of Chinese type specimens from the University Herbarium, University of California, the Harvard University Herbaria and the William and Lynda Steere Herbarium of New York Botanical Garden led to the discovery of errors in the designation of type specimens in the protologues of several names. Following Article 9.2 of the International Code of Nomenclature for algae, fungi, and plants (Shenzhen Code, 2018), typographical errors in the citation of collection numbers in the protologues of 23 Chinese vascular plants were corrected.

Dual nomenclature to be supported explicitly in the International Code of Nomenclature for algae, fungi, and plants

ABSTRACT Dual nomenclature as applied to dinoflagellates is underpinned by conceptual and practical considerations. It allows the separate naming of fossil- and non-fossil species even when they are linked to one another by incubation studies and other techniques. It is needed because fossil- and non-fossil taxonomies are based on different stages of the life cycle and cannot be integrated at the generic level. All taxonomists today who study dinoflagellates, whether living or fossil, place their work under the International Code of Nomenclature for algae, fungi, and plants. The Shenzhen Code and its predecessors have supported dual nomenclature implicitly with the help of examples, but without clear explanation of what it is and how it works. In Madrid, Spain in July 2024, the Nomenclature Section of the XX International Botanical Congress approved two new articles for the Code that remove earlier contradictions and introduced dual nomenclature explicitly, drawing on a critical distinction between ‘synonymy’ and the new concept and term ‘taxonomic equivalence’. These changes will be incorporated into the forthcoming Madrid Code. In addition to placing the Code in its historical context, we explain how it is amended in order to demystify an intricate but important procedure.

Synopsis of proposals on fungal nomenclature: a review of the proposals concerning Chapter F of the International Code of Nomenclature for algae, fungi, and plants submitted to the XII International Mycological Congress, 2024

A commentary is provided on the seven formally published proposals to modify the provisions of Chapter F of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) that will be dealt with by the Fungal Nomenclature Session (FNS) of the 12th International Mycological Congress (IMC12) in August 2024. The proposals deal with: fungi whose morph-names have the same epithet; the listing of synonyms under entries for protected names in the Code Appendices; the processes of protection and rejection; the use of DNA sequences as nomenclatural types; the use of genomes as nomenclatural types; and the designation of fungi known only from DNA sequences. Information is also provided on the composition and role of the Fungal Nomenclature Bureau, the operation of the FNS and the pre-Congress Guiding vote.

Proposals for consideration at IMC12 to modify provisions related solely to fungi in Chapter F of the International Code of Nomenclature for algae, fungi, and plants

Seven proposals or sets of proposals to modify the provisions of Chapter F of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) have been received. These proposals are formally presented together here. The topics addressed relate to: fungi whose morph-names have the same epithet; the listing of synonyms under entries for protected names in the Code Appendices; the processes of protection and rejection; the use of DNA sequences as nomenclatural types; the use of genomes as nomenclatural types; and the designation of fungi known only from DNA sequences. In addition, a suggestion is included to update the mention of the World Directory of Culture Collections in Article 40.7 Note 4. A Synopsis of the formal proposals will be provided in early July 2024, and the mycological community will be invited to provide a guiding vote on the proposals with a closing date of 2 August 2024. Final decisions on the proposals will be made following debate at the Fungal Nomenclature Session of IMC12 in August 2024.

Typifications in American and Australasian Rhynchospora sect. Pauciflorae (Cyperaceae)

In this work, 17 lectotypifications are proposed for names related to Rhynchospora section Pauciflorae Kük. The lectotypifications are part of a nomenclatural revision of the section, which has not been revised since its creation by Kükenthal in 1949. Protologues and nomenclatural types were consulted online, in physical herbaria, or in libraries. These typifications are essential for the correct application of species names and synonyms in accordance with the principles of the International Code of Nomenclature for Algae, Fungi, and Plants.

Cultures as types and the utility of viable specimens for fungal nomenclature

The debates over the requirement of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) for a viable specimen to represent the name-bearing type material for a species or infraspecific taxon have a long history. Taxonomy of fungi commonly studied as living cultures exemplified by yeasts and moulds, strongly depend on viable reference material. The availability of viable cultures is also particularly useful for several groups of filamentous and dimorphic fungi. While the preservation of metabolically inactive cultures is permitted and recommended by the ICNafp, there is room for improvement. Below, we review the history and current status of cultures as the name-bearing type material under the Code. We also present a roadmap with tasks to be achieved in order to establish a stable nomenclatural system that properly manages taxa typified by viable specimens. Furthermore, we propose setting up rules and defining the nomenclatural status of ex-type cultures under Chapter F, the section of the ICNafp that includes provisions specific to names of fungi.

Report of the Special-purpose Committee on Names of Fungi with the Same Epithet, established at the XIX International Botanical Congress in Shenzhen, China

A Special-purpose Committee on Fungal Names with the Same Epithet was established at the XIX International Botanical Congress (IBC) in Shenzhen, China in 2017, with a mandate to report to the 12th International Mycological Congress (IMC) with recommendations on a preferred course of action with respect to names of pleomorphic fungi sharing the same epithet under the International Code of Nomenclature for algae, fungi, and plants. This report provides a synthesis of the deliberations from the Special-purpose Committee. We discuss the arguments for and against the proposed solution to the problems that have arisen regarding the nomenclature of fungi described in multiple morphs using the same epithet. We also propose a gentler method of addressing the problem using existing procedures.

Nomenclatural standards of spring barley cultivars bred by the Volga Scientific Research Institute of Selection and Seed-Growing named after P.N. Konstantinov

The article discusses the cultivars of spring two-row barley ‘Povolzhsky 22’, ‘Povolzhsky 49’, ‘Povolzhsky Yantar’, and ‘Povolzhsky Priz’ bred by the Volga Scientific Research Institute of Selection and Seed-Growing named after P.N. Konstantinov, a branch of the Samara Federal Research Center of the Russian Academy of Sciences. The article describes the morphological, biological and economic characteristics of the cultivars. To prepare herbarium specimens of nomenclatural standards, plant material of cultivars ‘Povolzhsky 22’, ‘Povolzhsky 49’, and ‘Povolzhsky Yantar’ was used. These cultivars are represented by one herbarium sheet each and duplicated by 2, 1 and 3 sheets, respectively. A herbarium specimen of cultivar ‘Povolzhsky Priz’ has also been prepared, although State Variety Testing of the cultivar was not completed in 2023. This herbarium specimen will be registered as the nomenclatural standard of the cultivar when the latter will be included in the State Register.All herbarium specimens include whole plants at the milky ripeness stage, ears at the waxy ripeness stage, and grain samples. Appropriate plants were collected in Pushkin, in the fields of the “Pushkin and Pavlovsk Laboratories of VIR” (St. Petersburg), and ears and grains were obtained from the Volga Scientific Research Institute of Selection and Seed-Growing named after P.N. Konstantinov (Samara Province).All materials used for preparing herbarium specimens of a cultivar are the offspring of plants obtained as a result of individual family selection. Herbarium specimens of nomenclatural standards, their duplicates and herbarium specimens of cultivar ‘Povolzhsky Priz’ were prepared in accordance with the recommendations of the International Code of Nomenclature of Cultivated Plants (ICNCP), registered in the VIR Herbarium database and transferred to the Herbarium of Cultivated Plants of the World, their Wild Relatives and Weeds (WIR) at the National Center for Plant Genetic Resources.

Results of the preliminary guiding vote (“mail vote”) on proposals to amend the International Code of Nomenclature for algae, fungi, and plants submitted to the XX International Botanical Congress, Madrid 2024

Results of the preliminary guiding vote (“mail vote”) on proposals to amend the <i>International Code of Nomenclature for algae, fungi, and plants</i> submitted to the <scp>XX</scp> International Botanical Congress, Madrid 2024

Distinct genome trichotomy in members of Hapalosiphonaceae is guided by habitat adaptation with Mastigocladus laminosus UU774 as a case study

The family Hapalosiphonaceae is grouped under subsection IV complying with International Code of Nomenclature for algae, fungi, and plants (ICN). This is a complex taxonomic group with often overlapping morphological traits. The members of this group have heterogeneous habitats and need urgent attention for de-entangling the taxon. The genome comparisons among 44 high quality drafts belonging to Hapalosiphonaceae suggests the presence of three distinct groups, one largely dominated by thermophiles (Group 1) and the other comprising of members of diverse habitats (Group 2). The third group is small with only 2 representative members (Group 3) are considered as outliers. The group containing members of diverse habitats are characterized by the presence of higher number of ORFan genes, mobilome and secondary metabolites genes. The thermophiles belonging to Group 1 are characterized by compact genome whereas the Group 2 genomes having diverse ecological habitat show genome expansion possibly due to recent acquisition. Comparison of synonymous and non-synonymous substitution of conserved genes suggest, members of Group 2 are undergoing relaxed purifying selection. There is a significant increase in the number of core genes (2075 for n = 35) when Group 1 organisms are considered alone compared to only 46 core genes when all three groups are taken together (n = 44). The presence of a huge pan genome (47,756) and a relatively tiny core genome (46) suggests that the taxon is an open and expanding. Members of Group 2 are distinct in coding for commercial metabolite shinorine that was visibly absent from other members of the Hapalosiphonaceae. Our RNAseq investigations on Mastigocladus laminosus UU774, a candidate of Group 2, showed that metabolic clusters overexpressed during stress. UU774 metabolic extracts shown potential antibacterial and anticancer cell line activity.

Nomenclatural standards of barley cultivars bred by the Ural Research Institute of Agriculture – Branch of the Ural Federal Agrarian Scientific Research Center, Ural Branch of the Russian Academy of Sciences

As part of the present work, nomenclatural standards of spring barley cultivars ‘Krauf’ and ‘Pamyati Chepeleva’ were created by the Ural Research Institute of Agriculture.The plant material for these nomenclatural standards was collected at the Research and Production Base “Pushkin and Pavlovsk laboratories of VIR”.The article presents descriptions of morphological and biological and economic properties of the cultivars.The nomenclatural standard of cultivar ‘Krauf’ is represented by one herbarium sheet and has one duplicate sheet, while that of cultivar ‘Pamyati Chepeleva’ is represented by one herbarium sheet and two duplicates.Every sheet contains the entire plant at the milky ripeness stage collected at the Pushkin Laboratories of RPB “Pushkin and Pavlovsk Laboratories of VIR”, as well as mature spikes and grains samples collected at the Ural Research Institute of Agriculture. The plant material for the herbaria was taken from the offspring of one seed sample.The nomenclatural standard specimens were prepared in accordance with the recommendations of the International Code of Nomenclature of Cultivated Plants (ICNCP) and registered in the VIR Herbarium database. The herbarium specimens were deposited at the Herbarium of Cultivated Plants of the World, their Wild Relatives and Weeds (WIR) at the National Center for Plant Genetic Resources.

Validating Durio perakensis (Malvaceae) from Peninsular Malaysia

Durio perakensis Salma is described (together with a diagnosis) and typified to meet the requirements of the International Code of Botanical Nomenclature.

Commentary on the proposed Section 10 amendments to the International Code of Nomenclature of Prokaryotes regarding Candidatus names

Amendments were proposed to the International Code of Nomenclature of Prokaryotes (ICNP) in January [Arahal et al. (2024) Int. J Syst. Evol. Microbiol. 74: 006188] that would cause major changes in the treatment of Candidatus names. The amendments introduce Section 10 to name taxa whose names cannot be validly published under the ICNP because of the absence of type strains. This section creates a parallel ‘pro-nomenclature’ and formalizes alternative material which could serve as nomenclatural types. When conspecific isolates of taxa with Candidatus names are deposited in culture collections as type strains, the names can be validly published, and it is required that the same Candidatus name be used. While the amendments are promoted to provide stable names and rules of nomenclature for uncultivated taxa, the system is deeply flawed. It removes the permanent association between names and types, which will make the meaning of names imprecise and ambiguous. It creates ‘pro-nomenclature’, which is confusing and unnecessary. Since many taxa which cannot be validly named under the ICNP can already be named under the SeqCode, it duplicates and creates overlap with an established nomenclatural system without providing tangible benefits. As the SeqCode recognizes names formed under the ICNP, the ICNP should recognize names formed under the SeqCode as they have done for the Cyanobacteria named under the International Code of Nomenclature for algae, fungi and plants (ICN). For these reasons, we urge the members of the International Committee of Systematics of Prokaryotes (ICSP) to reject these amendments.