Taxonomic Proposals Research Articles

Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2024).

This article reports changes to virus taxonomy and taxon nomenclature that were approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2024. The entire ICTV membership was invited to vote on 203 taxonomic proposals that had been approved by the ICTV Executive Committee (EC) in July 2023 at the 55th EC meeting in Jena, Germany, or in the second EC vote in November 2023. All proposals were ratified by online vote. Taxonomic additions include one new phylum (Ambiviricota), one new class, nine new orders, three new suborders, 51 new families, 18 new subfamilies, 820 new genera, and 3547 new species (excluding taxa that have been abolished). Proposals to complete the process of species name replacement to the binomial (genus + species epithet) format were ratified. Currently, a total of 14,690 virus species have been established.

Phylogenomic analysis reveals the evolutionary history of Paleartic needle-leaved junipers

Needle-leaved junipers (Juniperus sect. Juniperus, Cupressaceae) are coniferous trees and shrubs with red or blue fleshy cones. They are distributed across Asia, Macaronesia and the Mediterranean Basin, with one species (J. communis) having a circumboreal distribution. Here we aim to resolve the phylogeny of this clade to infer its intricate evolutionary history. To do so, we built a comprehensive, time-calibrated phylogeny using genotyping-by-sequencing (GBS) and combine it with species occurrence using phylogeographic tools. Our results provide solid phylogenetic resolution to propose a new taxonomic classification and a biogeographical history of the section. Specifically, we confirm the monophyly of two groups within J. sect. Juniperus: the Asian (blue-cone) species including the circumboreal J. communis, and the Mediterranean-Macaronesian (red-cone) species. In addition, we provide strong phylogenetic evidence for three distinct species (J. badia, J. conferta, J. lutchuensis) previously considered subspecies or varieties, as well as for the differentiation between the eastern and western Mediterranean lineages of J. macrocarpa. Our findings suggest that the Mediterranean basin was the primary center of diversification for Juniperus sect. Juniperus, followed by an East Asian-Tethyan disjunction resulting from uplifts of the Qinghai-Tibetan Plateau and climatic shifts. The colonization history of Macaronesia by red-cone junipers from the western Mediterranean appears to have taken place independently in two different geological periods: the Miocene (Azores) and the Pliocene (Madeira-Canary Islands). Overall, genomic data and phylogenetic analysis are key to consider a new taxonomic proposal and reconstruct the biogeographical history of the iconic needle-leaved junipers across the Paleartic.

Contribution to knowledge of the oribatid mite genus Oribatodes (Acari, Oribatida, Cepheusidae), with supplementary descriptions of two species and data on juvenile instars

The supplementary descriptions of two species of Oribatodes (Oribatida, Cepheusidae), O. mirabilis Banks, 1895 and O. reticulatus (Sitnikova, 1979), are presented, based on adults collected from the U.S.A. and Panama, respectively. The deutonymphal and tritonymphal instars of O. mirabilis and the deutonymphal instar of O. reticulatus are described; this is the first data on juveniles of the genus. The revised generic diagnosis and an identification key to the known representatives of Oribatodes are provided. The taxonomic status of the related genus Reticulocepheus Vasiliu & Călugăr, 1977 is discussed, resulting in the following new taxonomic proposals: Oribatodes Banks, 1895 (=Reticulocepheus Vasiliu & Călugăr, 1977 syn. nov.); O. areolatus (Sitnikova, 1979) comb. nov.; O. decoui (Vasiliu & Călugăr, 1977) comb. nov.; O. grandis (Sitnikova, 1979) comb. nov.; O. mirabiloides (Jacot, 1938) comb. nov.; and O. reticulatus (Sitnikova, 1979) comb. nov. Comparative characteristics of juveniles of the different genera of Cepheusidae are given based on our own data and available literature sources.

A taxonomic proposal for cedratviruses, orpheoviruses, and pithoviruses.

Orpheoviruses, cedratviruses, and pithoviruses are large DNA viruses that cluster together taxonomically within the order Pimascovirales of the phylum Nucleocytoviricota. However, they were not classified previously by the International Committee on Taxonomy of Viruses (ICTV). Here, we present a comprehensive analysis of the gene content, morphology, and phylogenomics of these viruses, providing data that underpinned the recent proposal to establish new taxa for their initial classification. The new taxonomy, which has now been ratified by the ICTV, includes the family Orpheoviridae and genus Alphaorpheovirus, the family Pithoviridae and genus Alphapithovirus, and the family Cedratviridae and genus Alphacedratvirus, aiming to formally catalogue the isolates covered in this study. Additionally, as per the newly adopted rules, we applied standardized binomial names for the virus species created to classify isolates with complete genome sequences available in public databases at the time of the proposal. The specific epithet of each virus species was chosen as a reference to the location where the exemplar virus was isolated.

An architectural taxonomic proposal for passive design strategies used in traditional architecture of areas with hot and dry climates

Global environmental problems are one of the most critical problems of humankind. Increasing energy consumption and CO2 emissions are among the most important causes of global environmental problems. The existing building sector is vital in increasing energy consumption and CO2 emissions. Buildings are responsible for 30% of greenhouse gas emissions and about 40% of energy consumption. Energy used for heating and cooling is one of the most important causes of energy consumption in the building sector. Reducing the energy used for heating and cooling is possible with sustainable building design. One of the most essential criteria of sustainable building design is using passive air conditioning strategies. Traditional architecture is a crucial guide for using passive air conditioning elements. This paper presents an architectural taxonomic proposal for passive cooling strategies used in traditional architecture in hot and dry climate areas of the globe. The aim is to facilitate and simplify access to all cooling strategies and provide a guide for their adaptation to modern architecture. A total of 55 passive cooling strategies were identified in the research. Within the taxonomic proposal's scope, the strategy was first divided into four groups: settlement scale, building scale, space scale, and building environment scale, depending on the usage criteria. Then, this grouping was split into 16 subgroups. A taxonomic proposal was created by considering the intended use of the identified strategies. The findings indicate that although traditional architecture in hot and dry climates primarily focuses on heat protection and heat dissipation is also highly utilized. It has been determined that thermal insulation, shading and natural ventilation cooling strategies come to the fore. In addition, it has been determined that approximately 50% of the strategies used for cooling purposes are related to thermal insulation, shading, and natural ventilation. The taxonomic proposal guides modern adaptations in the built environment by combining traditional passive design strategies and simplifying their use. It can also be adapted to different climates and contribute to creating new modern building design guidelines.

The identities of three plants of unknown origin revealed by ancient paintings

AbstractArchives and correspondences are often overlooked resources in assessing taxonomic and nomenclatural information and this sometimes affects taxonomic proposals. Here we show that unpublished illustrations not only can definitively help in identifying unresolved or poorly known names but can be themselves original material and sometimes must serve as types, avoiding neotypes or misleading synonymizations. We present the case of three names introduced by the Neapolitan botanist Michele Tenore (Muscari strangwaysii, Asparagaceae; Pogostemon suavis and Salvia menthifolia, Lamiaceae). They have been interpreted differently over time because herbarium specimens that constituted original material were not accurately searched for (M. strangwaysii) or were unavailable (P. suavis, S. menthifolia). Although these three names are currently synonymized (with M. neglectum, P. cablin, and S. chamaedryoides) we demonstrate that these synonymies are not correct, based on the detailed study of original nineteenth‐century watercolour paintings, a re‐examination of protologues and specimens preserved in the Botanical Garden of Naples (NAP). The watercolour paintings are crucial for application of the names, because diagnostic features often disappear with drying (M. strangwaysii), or because they are the only extant original material (P. suavis). In all three cases we introduce new typifications for the names and update the synonymy to M. botryoides, P. heyneanus, and S. microphylla, respectively.

Valid publication of names of two domains and seven kingdoms of prokaryotes.

The International Code of Nomenclature of Prokaryotes (ICNP) now includes the categories domain and kingdom. For the purpose of the valid publication of their names under the ICNP, we consider here the two known domains, 'Bacteria' and 'Archaea', as well as a number of taxa suitable for the rank of kingdom, based on previous phylogenetic and taxonomic studies. It is proposed to subdivide the domain Bacteria into the kingdoms Bacillati, Fusobacteriati, Pseudomonadati and Thermotogati. This arrangement reflects contemporary phylogenetic hypotheses as well as previous taxonomic proposals based on cell wall structure, including 'diderms' vs. 'monoderms', Gracilicutes vs. Firmicutes, 'Negibacteria' vs. 'Unibacteria', 'Hydrobacteria' vs. 'Terrabacteria', and 'Hydrobacterida' vs. 'Terrabacterida'. The domain Archaea is proposed to include the kingdoms Methanobacteriati, Nanobdellati and Thermoproteati, reflecting the previous division into 'Euryarchaeota', 'DPANN superphylum' and 'TACK superphylum'.

Emerging materials for transition: A taxonomy proposal from a design perspective

In response to environmental challenges, design promotes emerging materials connected with the circular economy and environmental sustainability. However, there is confusion about their definition and contribution to sustainable design and production, showing a gap in their classification. This article proposes a taxonomy as a helpful tool to consolidate and unify terminology, definitions and general understanding of these emerging materials. An analysis of 31 real-world case studies helped outline the taxonomic proposal to formalise knowledge, fostering clarity in classifying and identifying them. The taxonomy aims to organise emerging materials, generate reflections, and encourage their responsible development, diffusion, and adoption.

Phylogenetic analysis of the Cladophora coelothrix complex, including the description of the new genus Leliaertia (Cladophorales, Ulvophyceae)

ABSTRACT Molecular phylogenetic studies have revealed the polyphyletic nature of Cladophora as traditionally circumscribed, which is separated into four main clades: Cladophoraceae, Siphonocladus, Pithophoraceae and Pseudocladophoraceae. Several taxonomic proposals have recently been made to resolve its polyphyletic nature. The present work focuses on the cryptic diversity of Cladophora coelothrix, within the Siphonocladus clade. Based on new collections from northeastern Brazil and phylogenetic analyses of partial SSU and LSU rDNA sequence alignments, we propose the new genus and species Leliaertia repens to accommodate one of the cryptic species hitherto included in C. coelothrix, occurring in the tropical Atlantic, Indian and Pacific Oceans. Leliaertia repens was recovered in the Siphonocladus clade and is phylogenetic distinct from the genuine Cladophora species in the Cladophoraceae. The new species occurs in marine and estuarine environments and forms conspicuous mats of semi-prostrate filaments. It represents a cryptic species and genus since morphological features, including the diameter and length:diameter ratio of the apical cell, show high levels of overlap with other species, including C. socialis. Our phylogenetic data indicate that L. repens, C. coelothrix and C. socialis represent a complex of cryptic species with at least four lineages, some of which co-occur in tropical seas.

Molecular evidence to support the transfer of Enteromorpha ovata to genus Ulva and evaluate its divergence using multi‐locus time‐calibrated phylogeny

Ulva has received considerable attention since its merger with tubular Enteromorpha (Linnaeus) Nees based on molecular evidence. Nevertheless, several nomenclatural and taxonomic proposals concerning tropical and subtropical species are still pending in want of investigations based on the altered circumscription and criteria of genetic diversity. Enteromorpha ovata Thivy et Visalakshmi ex H. Joshi et V. Krishnamurthy has a restricted geographical distribution only at Gopnath, India. In the present study, we for the first time provide a polyphasic approach to ascertain its taxonomic position, using morpho‐anatomy, ecology and molecular taxonomy with multigene markers (rbcL, tufA and ITS rDNA). Phylogenetic analysis based on rbcL, tufA and ITS rDNA gene sequences supported the recognition of this species within the genus Ulva. The recent revision by Kumar and Palanisamy proposed the new nomenclatural combinaton Ulva ovata (Thivy et Visalakshmi ex Joshi et Krishnamurthy) Aron Santhosh Kumar and Palanisamy, but they did not give molecular evidence while doing so, which we accomplished. Our time‐calibrated phylogeny suggested that U. ovata diverged from its respective sister lineages ~ 4.46 Mya in the Neogene period of the Cenozoic Era.

Phylogenetic discordance and integrative species delimitation in the Mammillaria haageana species complex (Cactaceae)

Species complexes consist of very close phylogenetic relatives, where morphological similarities make it difficult to distinguish between them using traditional taxonomic methods. Here, we focused on the long-standing challenge of species delimitation in the Mammillaria haageana complex, a group that presents great morphological diversity that makes its taxonomy a puzzle. Our work integrates genomic, morphological, and ecological data to establish the taxonomic limits in the M. haageana complex, and we also studied the evolutionary relationships with the remainder of the M. ser. Supertextae species. Our genetic analyses, as well as morphological and ecological evidence, led us to propose that the M. haageana complex is made up of six distinct entities (M. acultzingensis, M. conspicua, M. haageana, M. lanigera, M. meissneri, and M. san-angelensis), mainly as a result of ecological speciation. A recent taxonomic proposal considered these taxa as a single species; therefore, we propose their recognition at the species level. Our results also show a high level of incomplete lineage sorting rather than reticulation, which is especially likely in recently diverged species such as those comprising M. ser. Supertextae. The species hypotheses proposed here may be useful in future extinction risk assessments and conservation strategies.

Molecular systematics of tamarins with emphasis on genusTamarinus(Primates, Callitrichidae)

AbstractThe genusSaguinuscomprises three principal clades that diverged in the Middle to Late Miocene. Their taxa are ecologically differentiated and allopatrically distributed. These clades were recently recognized as different genera,Saguinus,TamarinusandOedipomidas. InTamarinus, the phylogenetic relationships among species/subspecies are poorly understood. Thus, in this study we present a comprehensive dated genomic phylogeny based on double digest restriction associated DNA for all known species and subspecies ofTamarinus. We also tested whether thatTamarinus imperatorandTamarinus subgrisescensare different species, as morphology‐based taxonomy, phenotypical divergences and mitochondrial genes recognized them as two different species. Additionally, we reconstructed time‐calibrated phylogenetics tree hypotheses of all extant species and subspecies of the generaSaguinus,TamarinusandOedipomidas. Our analysis robustly supported the phylogenetic hypothesis of all species/subspecies of the genusTamarinus; strongly supported a divergence between the three clades,Saguinus,OedipomidasandTamarinus; and provided support forT. imperatorandT. subgrisescensas distinct species. Therefore, we reiterate and ratify the division ofSaguinusinto three genera, supporting the taxonomic proposal for these genera.

Changes to virus taxonomy and the ICTV Statutes ratified by the International Committee on Taxonomy of Viruses (2023).

This article reports changes to virus taxonomy and taxon nomenclature that were approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in April 2023. The entire ICTV membership was invited to vote on 174 taxonomic proposals that had been approved by the ICTV Executive Committee in July 2022, as well as a proposed revision of the ICTV Statutes. All proposals and the revised ICTV Statutes were approved by a majority of the voting membership. Of note, the ICTV continued the process of renaming existing species in accordance with the recently mandated binomial format and included gene transfer agents (GTAs) in the classification framework by classifying them as viriforms. In total, one class, seven orders, 31 families, 214 genera, and 858 species were created.

Virus taxonomy and the role of the International Committee on Taxonomy of Viruses (ICTV).

The taxonomy of viruses is developed and overseen by the International Committee on Taxonomy of Viruses (ICTV), which scrutinizes, approves and ratifies taxonomic proposals, and maintains a list of virus taxa with approved names (https://ictv.global). The ICTV has approximately 180 members who vote by simple majority. Taxon-specific Study Groups established by the ICTV have a combined membership of over 600 scientists from the wider virology community; they provide comprehensive expertise across the range of known viruses and are major contributors to the creation and evaluation of taxonomic proposals. Proposals can be submitted by anyone and will be considered by the ICTV irrespective of Study Group support. Thus, virus taxonomy is developed from within the virology community and realized by a democratic decision-making process. The ICTV upholds the distinction between a virus or replicating genetic element as a physical entity and the taxon category to which it is assigned. This is reflected by the nomenclature of the virus species taxon, which is now mandated by the ICTV to be in a binomial format (genus + species epithet) and is typographically distinct from the names of viruses. Classification of viruses below the rank of species (such as, genotypes or strains) is not within the remit of the ICTV. This article, authored by the ICTV Executive Committee, explains the principles of virus taxonomy and the organization, function, processes and resources of the ICTV, with the aim of encouraging greater understanding and interaction among the wider virology community.

Pending Reorganization of Hantaviridae to Include Only Completely Sequenced Viruses: A Call to Action.

The official classification of newly discovered or long-known unassigned viruses by the International Committee on Taxonomy of Viruses (ICTV) requires the deposition of coding-complete or -near-complete virus genome sequences in GenBank to fulfill a requirement of the taxonomic proposal (TaxoProp) process. However, this requirement is fairly new; thus, genomic sequence information is fragmented or absent for many already-classified viruses. As a result, taxon-wide modern phylogenetic analyses are often challenging, if not impossible. This problem is particularly eminent among viruses with segmented genomes, such as bunyavirals, which were frequently classified solely based on single-segment sequence information. To solve this issue for one bunyaviral family, Hantaviridae, we call on the community to provide additional sequence information for incompletely sequenced classified viruses by mid-June 2023. Such sequence information may be sufficient to prevent their possible declassification during the ongoing efforts to establish a coherent, consistent, and evolution-based hantavirid taxonomy.

Putative Mitoviruses without In-Frame UGA(W) Codons: Evolutionary Implications.

Mitoviruses are small vertically transmitted RNA viruses found in fungi, plants and animals. Taxonomically, a total of 105 species and 4 genera have been formally recognized by ICTV, and recently, 18 new putative species have been included in a new proposed genus. Transcriptomic and metatranscriptomic studies are a major source of countless new virus-like sequences that are continually being added to open databases and these may be good sources for identifying new putative mitoviruses. The search for mitovirus-like sequences in the NCBI databases resulted in the discovery of more than one hundred new putative mitoviruses, with important implications for taxonomy and also for the evolutionary scenario. Here, we propose the inclusion of four new putative members to the genus Kvaramitovirus, and the existence of a new large basally divergent lineage composed of 144 members that lack internal UGA codons (subfamily "Arkeomitovirinae"), a feature not shared by the vast majority of mitoviruses. Finally, a taxonomic categorization proposal and a detailed description of the evolutionary history of mitoviruses were carried out. This in silico study supports the hypothesis of the existence of a basally divergent lineage that could have had an impact on the early evolutionary history of mitoviruses.

On the identity of Opuntia elata s.l. (Cactaceae) introduced in the Mediterranean region. A taxonomic and nomenclatural update

Opuntia elata and O. monacantha are the two species of Opuntia Series Armatae traditionally accepted as naturalized in the Mediterranean region and Europe. However, a review based on the analysis of the available images and on the criteria of the most recent taxonomic proposals shows that O. elata s.s. is not present. The plants so far assigned to O. elata belong to O. bonaerensis, a clearly differentiated species, or to O. rioplatensis and O. canterae, both species similar to O. elata and recently segregated. The situation looks similar for South Africa and Australia, where the iconography shows other species of this group but not O. elata in the strict sense.

Re-evaluating and dating myriapod diversification with phylotranscriptomics under a regime of dense taxon sampling

Recent transcriptomic studies of myriapod phylogeny have been based on relatively small datasets with <40 myriapod terminals and variably supported or contradicted the traditional morphological groupings of Progoneata and Dignatha. Here we amassed a large dataset of 104 myriapod terminals, including multiple species for each of the four myriapod classes. Across the tree, most nodes are stable and well supported. Most analyses across a range of gene occupancy levels provide moderate to strong support for a deep split of Myriapoda into Symphyla + Pauropoda (=Edafopoda) and an uncontradicted grouping of Chilopoda + Diplopoda (=Pectinopoda nov.), as in other recent transcriptome-based analyses; no analysis recovers Progoneata or Dignatha as clades. As in all recent multi-locus and phylogenomic studies, chilopod interrelationships resolve with Craterostigmus excluded from Amalpighiata rather than uniting with other centipedes with maternal brood care in Phylactometria. Diplopod ordinal interrelationships are largely congruent with morphology-based classifications. Chilognathan clades that are not invariably advocated by morphologists include Glomerida + Glomeridesmida, such that the volvation-related characters of pill millipedes may be convergent, and Stemmiulida + Polydesmida more closely allied to Juliformia than to Callipodida + Chordeumatida. The latter relationship implies homoplasy in spinnerets and contradicts Nematophora. A time-tree with nodes calibrated by 25 myriapod and six outgroup fossil terminals recovers Cambrian–Ordovician divergences for the deepest splits in Myriapoda, Edafopoda and Pectinopoda, predating the terrestrial fossil record of myriapods as in other published chronograms, whereas age estimates within Chilopoda and Diplopoda overlap with or do not appreciably predate the calibration fossils. The grouping of Chilopoda and Diplopoda is recovered in all our analyses and is formalized as Pectinopoda nov., named for the shared presence of mandibular comb lamellae. New taxonomic proposals for Chilopoda based on uncontradicted clades are Tykhepoda nov. for the three blind families of Scolopendromorpha that share a “sieve-type” gizzard, and Taktikospina nov. for Scolopendromorpha to the exclusion of Mimopidae.

A Survey of Virtualization Technologies: Towards a New Taxonomic Proposal

At present, there is a proliferation of virtualization technologies (VTs), which are part of the basic and underlying infrastructure of popular cloud computing. Those interested in VTs are faced with a non-unified volume of information and various approaches to modes of operation, classification structures, and the performance implications of these technologies. This makes it difficult to decide which type of VT is appropriate for a particular context. Therefore, this paper reviews the state of the art on VT taxonomic models. Methodologically, a literature review is carried out to identify VT classification models, recognizing their features and weaknesses. With this in mind, a new taxonomy of virtualization technologies is proposed, which responds to the weaknesses identified in the analyzed schemes. The new VT taxonomy combines the Abstraction Level and Virtual Machine Type approaches, providing the reader with a means to visualize VTs. In doing so, the reader can locate the level of abstraction at which each VT is developed, in addition to the type of machine projected, whether it is a complete system or an execution environment for processes. The proposed taxonomy can be used in the academic environment to facilitate teaching processes or in the business environment to facilitate decision-making when implementing VTs.

Recent changes to virus taxonomy ratified by the International Committee on Taxonomy of Viruses (2022).

This article reports the changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses (ICTV) in March 2022. The entire ICTV was invited to vote on 174 taxonomic proposals approved by the ICTV Executive Committee at its annual meeting in July 2021. All proposals were ratified by an absolute majority of the ICTV members. Of note, the Study Groups have started to implement the new rule for uniform virus species naming that became effective in 2021 and mandates the binomial 'Genus_name species_epithet' format with or without Latinization. As a result of this ratification, the names of 6,481 virus species (more than 60 percent of all species names currently recognized by ICTV) now follow this format.