Nomenclatural Types Research Articles

An overview of Astrocaryum (Bactridinae, Arecaceae) types from Brazil described by João Barbosa Rodrigues

João Barbosa Rodrigues, a renowned Brazilian botanist, spent years intensively studying Orchidaceae and Arecaceae and oversaw two important institutions in Brazil: the Museu Botânico do Amazonas and the Jardim Botânico do Rio de Janeiro. However, when it comes to his taxonomic studies, there are controversies about the existence of specimens mentioned in the protologues of his new species. For example, for the palm genus Astrocaryum, several issues have arisen regarding identifying and designating nomenclatural types of the species he described. Different researchers presumed that the entire collection of types was destroyed after the Museu Botânico do Amazonas closed and due to natural disasters, that affected his collections in city of Rio de Janeiro. Thus, in this study we investigated the names of Astrocaryum described by Barbosa Rodrigues. We conducted a comprehensive investigation of Barbosa Rodrigues’ works to determine the origin and current location of the possible nomenclatural types associated with the Astrocaryum species he described. Additionally, we reviewed the designations proposed by Jan Wessels Boer and Sidney Glassman for these species in the previous century. Based on our thorough search, we confirmed the absence of the specimens mentioned in the protologues of these species. Furthermore, we substantiated the typifications made by Wessels Boer and Glassman, which were based on illustrations by Barbosa Rodrigues. Our findings confirm the assignment of six lectotypes and twelve neotypes for Astrocaryum based on the Shenzhen Code.

Proposal of Patescibacterium danicum gen. Nov., sp. nov. in the ubiquitous ultrasmall bacterial phylum Patescibacteriota phyl. Nov

Abstract Candidatus Patescibacteria is a diverse bacterial phylum that is notable for members with ultrasmall cell size, reduced genomes, limited metabolic capabilities and dependence on other prokaryotic hosts. Despite the prevalence of the name Ca. Patescibacteria in the scientific literature, it is not officially recognized under the International Code of Nomenclature of Prokaryotes (ICNP) and lacks a nomenclatural type. Here, we rectify this situation by describing two closely related circular metagenome-assembled genomes (MAGs) and by proposing one of them (ABY1TS) to serve as the nomenclatural type for the species Patescibacterium danicumTS gen. Nov., sp. nov. according to the rules of the SeqCode. Rank-normalized phylogenomic inference confirmed the stable placement of P. danicumTS in the class ABY1 within Ca. Patescibacteria. Based on these results, we propose Patescibacterium gen. Nov. to serve as the type genus for associated higher taxa, including the phylum Patescibacteriota phyl. Nov. We complement our proposal with a genomic characterization, metabolic reconstruction, and biogeographical analysis of Patescibacterium. Our results confirm small genome sizes (< 1Mbp), low GC content (>36%), and the occurrence of long gene coding insertions in the 23S rRNA sequences, along with reduced metabolic potential, inferred symbiotic lifestyle, and a global distribution. In summary, this effort, focused on the fourth-largest phylum in the bacterial domain, aims to provide nomenclatural stability in the scientific literature.

Synopsis of the genus <i>Polystemma</i> (Apocynaceae, Asclepiadoideae) and recognition of three new species

Background: Polystemma is characterized by a mixed indumentum of glandular trichomes that turn white, rotate to rotate-campanulate corollas, a gynostegial corona with filiform appendages, and fusiform follicles. The taxon has undergone numerous taxonomic changes in recent years. In current phylogenies, Polystemma has been recovered as paraphyletic and many of its species require a new combination. In this study, we propose the corresponding changes and describe, map, and illustrate three new species within this genus. Questions: Do morphological data support the transfer of Matelea species to Polystemma? Are the plants of Polystemma collected in Durango, Jalisco, and Sinaloa different species? Studied species: Polystemma. Study site and dates: United States, Mexico, Guatemala, El Salvador, Honduras, Nicaragua y Costa Rica, between 2022 and 2024. Methods: More than 3,000 specimens from 20 herbaria and virtual databases were reviewed. Distribution maps were generated, and risk categories were proposed. The cohesive species concept was proposed as an explanatory hypothesis for taxon recognition. Results: A total of 27 species of the genus were recognized, these distributed from the southeastern United States of America to Costa Rica. Eleven new combinations and three lectotypifications are made, and three new species for science are proposed. Identification key, nomenclatural type information, synonyms, habitat, images of all species and distribution maps are also included. Conclusions: The review of this genus allowed for updating and improving the systematics within the subtribe Gonolobinae. Likewise, it highlights Mexico as the center of diversity and endemism for Polystemma.

Nomenclature notes on vegetation of the Salicetea purpureae Moor 1958 class in Ukraine

A brief history of the syntaxonomic studies of floodplain vegetation of the Salicetea purpureae class in Ukraine is presented and the tasks of further research are established. Our study has shown that the vegetation of the class includes more than 30 associations, which belong to 6 alliances and 2 orders. According to the ecological peculiarities, they are divided into willow shrubs on the gravel banks of streams in the montane and subalpine belts of the temperate and boreal zones of Europe and the Caucasus (Salicion eleagno-daphnoidis), willow and poplar forests of lowland and foothill rivers formed on alluvium in the nemoral zone of Europe and at high altitudes in the Mediterranean region (Salicion albae), willow shrubs on the sandy-loamy soils of the river banks of lowlands and foothills of the nemoral zone of Europe (Salicion triandrae), willow shrubs on riverine dunes in central Ukraine (Artemisio dniproicae-Salicion acutifoliae), shrubs on temporarily flooded clay soils in central Ukraine (Rubo caesi-Amorphion fruticosae). The problems of using the phytosociological nomenclature during the analysis of the Salicetea purpureae vegetation on the territory of Ukraine are highlighted. It was found that half of the syntaxa listed in Ukrainian geobotanical literature are synonyms, published invalidly, or need typification. Every syntaxon is accompanied by explanations of its non-validity with citations of the relevant articles published in the 4th edition of the International Code of Phytosociological Nomenclature. In addition to the incorrectly cited associations, two of the six alliances (Artemisio dniproicae-Salicion acutifoliae, Rubo caesii-Amorphion fruticosae) also require correction because their description was based on the invalid nomenclatural types formed by the selection of species which are invalid according to The Euro+Med PlantBase. In this paper, we aimed to analyze the studies on the vegetation of the Salicetea purpureae class on the territory of Ukraine using the Braun–Blanquet approach, determine the issues that require more detailed research in the future, and make some notes on nomenclature discordances. Such review makes it possible to determine all mismatches in phytosociological nomenclature.

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.

Psilotum (Psilotaceae-Ophioglossales): a taxonomic assessment based on morpho-anatomical studies of the species from the Neotropics

The recent discovery of Psilotum × intermedium in Mexico prompted us to reassess the nomenclature of this genus, which has global implications. From an extensive review of nomenclatural types and herbarium specimens, field collections, and a morpho-anatomical analysis, P. nudum and P. flaccidum are treated as accepted species, while P. × complanatum is treated as an interspecific hybrid between them. With this clarification, we specify their main synonymies and designate seven lectotypes (for Bernhardia schiedeana, Psilotum complanatum var. latissimum, P. complanatum var. mexicanum, P. floridanum, P. neocaledonicum, P. triquetrum, P. triquetrum var. gracile) and we select an epitype to give taxonomic support to the hybrid. We provide descriptions, diagnostic comments, and a key for identification of the accepted taxa, and also update the geographical ranges of these three taxa, mainly in Neotropics.

SeqCode: A Nomenclatural Code for Prokaryotes.

SeqCode is a nomenclatural code for naming prokaryotes based on genetic information. With the majority of prokaryotes being inaccessible as pure cultures, they are not eligible for naming under the International Code of Nomenclature of Prokaryotes. To address this challenge, a new concept that is SeqCode, which assign names to prokaryotes on the basis of genome sequence, has been announced in 2022. The valid publication of names for prokaryotes based on isolated genome, metagenome-assembled genomes, or single-amplified genome sequences. It operates through a registration portal, SeqCode Registry, where metadata is linked to names and nomenclatural types. This code provides a framework for reproducible nomenclature for all prokaryotes, either culturable or not and facilitates communication across all microbiological disciplines. Additionally, the SeqCode includes provisions for updating and revising names as new data becomes available. By providing a standardized system for naming and classifying these microorganisms based on their genetic information, the SeqCode will facilitate the discovery, understanding and comparison of these microorganisms, helping us to understand their role in the environment and how they contribute to the functioning of the Earth.

Nomenclature and typification of plant names related to Centaureaaplolepa and C.leucophaea (Asteraceae) from Italy and France.

Centaureaaplolepa Moretti and C.leucophaea Jord. (Asteraceae) are endemic to the central-western Mediterranean and include, respectively, ten and six subspecies, mostly occurring in north-western Italy and south-eastern France. As part of an ongoing systematic study on CentaureaL.sect.Centaurea from the central Mediterranean, 17 nomenclatural types (13 lectotypes, three neotypes and one epitype) are designated to fix the application of all names of the taxa described for France and Italy and related to C.aplolepa and C.leucophaea. In addition, previous typifications are critically revised and discussed. Centaureaaplolepasubsp.maremmana (Fiori) Dostál and C.litigiosa (Fiori) Arrigoni, two currently accepted taxa endemic to Tuscany (central Italy), are respectively considered here as heterotypic synonyms of C.aplolepasubsp.carueliana (Micheletti) Dostál and C.aplolepasubsp.cosana (Fiori) Dostál. Finally, C.aplolepasubsp.gallinariae (Briq. & Cavill.) Dostál, a currently accepted subspecies narrowly endemic to the Gallinara island (Liguria, northern Italy), is considered here as a heterotypic synonym of C.leucophaeasubsp.brunnescens (Briq.) Dostál.

Interpretation of lymphoid proliferations and lymphomas associated with immune deficiency and dysregulation in the 5th edition WHO classification of haematolymphoid tumours

The fifth edition of the World Health Organization (WHO) classification of lymphohematopoietic system tumors updated the terminology, types of lesions, diagnostic criteria, nomenclature, and other aspects of lymphoid proliferations and lymphomas associated with immune deficiency and dysregulation. The important updates and main changes in this section were briefly introduced, in order to guide the precise classification of lymphoid proliferations and lymphomas associated with immune deficiency and dysregulation, and standardize pathological reports.

Description of Asgardarchaeum abyssi gen. nov. spec. nov., a novel species within the class Asgardarchaeia and phylum Asgardarchaeota in accordance with the SeqCode

Asgardarchaeota, commonly referred to as Asgard archaea, is a candidatus phylum-rank archaeal clade that includes the closest archaeal relatives of eukaryotes. Despite their prevalence in the scientific literature, the name Asgardarchaeota lacks nomenclatural validation. Here, we describe a novel high-quality metagenome-assembled genome (MAG), AB3033_2TS, proposed to serve as the nomenclatural type for the species Asgardarchaeum abyssiTS according to the rules of the SeqCode. Based on protein content and compositional features, we infer that A. abyssi AB3033_2TS is an acetogenic chemoheterotroph, possibly a facultative lithoautotroph, and is adapted to a thermophilic lifestyle. Utilizing genomes from Asgard archaea, TACK, and Euryarchaea, we perform phylogenomic reconstructions using the GTDB archaeal marker genes, the current reference set for taxonomic classification. Calibrating relative evolutionary divergence (RED) values for Asgardarchaeota using established Thermoproteota lineages in the GTDB r207 reference tree, we establish a robust classification and propose Asgardarchaeum as the type genus for the family Asgardarchaeaceae (fam. nov)., the order Asgardarchaeales (ord. nov.), the class Asgardarchaeia (class. nov.), and the phylum Asgardarchaeota (phyl. nov.). This effort aims to preserve taxonomic congruence in the scientific literature.

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.

A phylogenetic reappraisal of Moorella and Thaxteriellopsis based on fresh material of the type species from India

ABSTRACT Moorella was described as an asexual genus of Ascomycota initially discovered in India and comprises three accepted morphospecies. The original nomenclatural type (holotype) of Moorella speciosa (Herb. Hyd. V. V. C. B. L. No. 297) was missing from the repository, and neither a possible lectotype nor isotypes were located; we therefore designate a sequenced neotype from India to fix the application of this name. Even though, Thaxteriellopsis was synonymised initially under Chaetosphaerulina, the type species T. lignicola, was later resurrected due to its unique sexual morph characteristics. Although various authors reported natural and cultural co-occurrences of Moorella and Thaxteriellopsis, the taxonomy had not been reassessed by molecular methods under the provisions of one fungus: one name. Phylogenies inferred from Maximum Likelihood analysis and Bayesian Inference of the combined ITS, LSU, TEF1α and RPB2 sequence data delineated Moorella and erstwhile Thaxteriellopsis accessions in a single clade within Tubeufiaceae. Based on this molecular study and the one fungus: one name rule, the genus Moorella has priority over Thaxterillopsis, and both T. lignicola and T. obliqua are placed in Moorella (as M. lignicola and M. obliqua).

Eugenia (Myrtaceae) from Reserva Natural Vale, Espírito Santo, a center of plant endemism in the Brazilian Atlantic Rainforest

Eugenia includes ca. 1,100 species worldwide and is the richest angiosperm genus of Brazilian flora with a remarkable biodiversity in the Atlantic Rainforest. In Espírito Santo state, the central-north region conserves the biggest forest fragment and is composed by the lowland coastal forests known as Tabuleiro. Considering the scarcity of studies approaching this vegetation and the high diversity of Eugenia species, this work presents a taxonomic treatment of Eugenia species from Reserva Natural Vale. The study area is located at the municipalities of Linhares and Sooretama, in the northern part of the coastal mesoregion of the state. For the taxonomic treatment, fieldwork was carried out between August 2015 and March 2019 and herbarium collections of BHCB, CVRD, CEPEC, ESA, HRCB, HPL, HUFSJ, ICN, K, MBM, MBML, RB, RBR, SORO, SP, SPF, SPSF, UB, UEC, and VIES were consulted, as well as images of nomenclatural types available online. This work points out the occurrence of 48 species of Eugenia within Reserva Natural Vale, encompassing 48% of the Eugenia species recorded in the Espírito Santo state. Six of them are presented as new occurrences for the reserve (Eugenia arenaria, E. disperma, E. florida, E. handroi, E. pachnantha and E. schottiana); two (E. pachnantha and E. schottiana) are first recorded for the state; E. adenophylla and E. infuscata are described as new. Eugenia adenophylla, E. atlantica, Eugenia cataphyllea, E. flavicarpa, E. hispidiflora, E. ochracea, E. penduliflora, and E. soteriana are endemic to Tabuleiro coastal forest, and E. handroi is the only record for Espírito Santo state. The most useful characters to distinguish the species are hair colours, especially in the floral structures, midvein on the adaxial surface of leaf blades, inflorescence type, connation and persistence of bracteoles, and the presence or absence of indumentum on the flowers’ hypanthia. Furthermore, morphological descriptions, distribution and phenology data, taxonomic comments, species illustrations, and an identification key for the species in the reserve are presented.

Plant Taxonomy - Its Past Role and Future Lines of Action in India

The history of floristic and taxonomic research in India is briefly reviewed and the decline and revival of floristic studies in India is traced.Modern concepts in plant taxonomy are towards the synthesis of orthodox taxonomic practices and modern methodologies. There need not be any clash between the so called alpha and omega taxonomists. All data that can be readily scanned for the species is useful for the taxonomist. The only aspect that has to be considered is the utillty of classification for a specified purpose. A field, or forest botanist needs diagnostic keys based on superficial morphological characters for identification of plants in the field. Characters based on anatomy, embryology chromosome structure and number, palynology, plant alkaloids and protein serum analysis are useful tools for finding out the systematic position of plants of doubtful affinity; however,. these characters cannot be readily used in the field for identification of plants. The herbarium identification of plants is the simple method of retrieval of plant identity through standard specimens properly authenticated by an expert. It does not give legality for the concept of fixity of species as wrongly alluded to by some non-taxonomists, since Nomenclatural Type is a constituent element of a taxon and it is not necessarily the most representative element.Some of the lines where taxonomists could play a major role are the inventory listing of plants for the conservation of species, monitoring rate of decline and spread of species, establishment of botanical record centres, environmental education and collaboration with universities for reorientation of teaching methods.The necessity for floristic training is stressed and a syllabus drawn up.

Cultivars of green bean for the Northwestern region of Russia

Based on the rules and recommendations of the International Code of Nomenclature for Cultivated Plants, nomenclatural standards were prepared for three green bean cultivars ‘Elizaveta’, ‘Uspekh’, and ‘Rebus’ bred at the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR). The nomenclatural standards were designed as herbarium sheets, three per cultivar for ‘Elizaveta’ and ‘Rebus’, and four sheets for cv. ‘Uspekh’. Each sheet contains parts of one plant supplemented with photographs of beans, seeds and flowers of each green bean cultivar. Nomenclatural standards were registered in the VIR Herbarium database and deposited in the nomenclatural types section of the Herbarium of cultivated plants of the world, their wild relatives and weeds (WIR) and the National Center for Plant Genetic Resources of Russia.

Taxonomic revision of Rhynchosia Lour. (Leguminosae, Papilionoideae, Phaseoleae) in South America

Rhynchosia Lour. has a pantropical distribution and comprises approximately 230 species, of which ca. 55 occur in the Neotropics and 31 in South America. The only existing taxonomic review that treated the South American species of the genus was carried out in 1978. It does not account for many new collections and several recently described species, and the delimitation of taxa remains problematic. Consequently, we undertook a comprehensive review of the South American species of Rhynchosia and present here a new taxonomic revision. The revision is based on our own fieldwork, extensive study of the relevant literature, and analysis of ca. 2000 herbarium collections including the nomenclatural types for all published names that have been linked to the South American taxa of Rhynchosia. Twenty-seven species are recorded for South America, where they are distributed in a variety of open and forested habitats, with the greatest diversity concentrated in the Cerrado domain. Most of the South American taxa are widely distributed in this region and some also occur in Central and North America. Rhynchosia minima is the only species in South America with a larger distribution that extends to the Old World. We provide an identification key, morphological descriptions for all of the recorded taxa, information about the nomenclatural types, synonyms, geographical distributions, habitats, phenology, and conservation status, as well as distribution maps, illustrations and photos of selected species in the field. We present six new synonymizations and 50 lectotypifications, of which 30 are second-step.

SeqCode facilitates naming of South African rhizobia left in limbo

South Africa is well-known for the diversity of its legumes and their nitrogen-fixing bacterial symbionts. However, in contrast to their plant partners, remarkably few of these microbes (collectively referred to as rhizobia) from South Africa have been characterised and formally described. This is because the rules of the International Code of Nomenclature of Prokaryotes (ICNP) are at odds with South Africa's National Environmental Management: Biodiversity Act and its associated regulations. The ICNP requires that a culture of the proposed type strain for a novel bacterial species be deposited in two international culture collections and be made available upon request without restrictions, which is not possible under South Africa’s current national regulations. Here, we describe seven new Mesorhizobium species obtained from root nodules of Vachellia karroo, an iconic tree legume distributed across various biomes in southern Africa. For this purpose, 18 rhizobial isolates were delineated into putative species using genealogical concordance, after which their plausibility was explored with phenotypic characters and average genome relatedness. For naming these new species, we employed the rules of the recently published Code of Nomenclature of Prokaryotes described from Sequence Data (SeqCode), which utilizes genome sequences as nomenclatural types. The work presented in this study thus provides an illustrative example of how the SeqCode allows for a standardised approach for naming cultivated organisms for which the deposition of a type strain in international culture collections is currently problematic.

Supplement to the Rubiaceae in the Flora dos Estados de Goiás e Tocantins, Brazil: Nomenclatural revision, typifications, new records, new identifications, and new combinations

The contribution of the family Rubiaceae for the Flora dos Estados de Goiás e Tocantins – Coleção Rizzo (FGT), published in November 2010, includes the treatment of 61 genera and 245 species. Nomenclatural types were cited in various ways, depending on the information and photographs available to the author before 2008. For numerous names, lectotype designations were not accompanied by “here designated” or a similar expression, which is required by the Internation Code of Nomenclature starting from 1 January 2001, therefore those designations are not valid. Also, the barcodes of type specimens were not cited in that treatment, because at that time, it was not common practice to cite that information, especially in floristic treatments, and also because barcodes were not yet assigned to specimens in many herbaria. The type citations are here corrected, type citations correctly cited with additional information added, and designate lectotypes or neotypes of names that still need to be designated, are deginated. A total of 81 lectotypifications and 11 neotypifications are here presented. A list of names newly typified is available in Appendix 1. Updates of the taxonomic and systematic changes that occurred during the last 15 years, are provided. Major changes regarding generic delimitations, mostly in the tribes Palicoureeae, Psychotriae, and Spermacoceeae, have recently been proposed, and numerous new combinations have recently been published by several authors, which are here included. Following those recent generic rearragements, three new combinations in Palicourea are here published, namely P. leiocarpa, P. stachyoides, and P. subtriflora.