Nomenclature Of Species Research Articles

Two Genetically Distinct yet Morphologically Indistinct Bungarus Species (Squamata, Elapidae) in Hong Kong

Kraits (genus Bungarus) are a group of highly venomous elapid snakes found across tropical Asia. Although they are notorious for causing many, often deadly, envenomations throughout the continent, their taxonomy and species nomenclature is subject to regular revisions. The boundaries demarcating B. candidus, B. multicinctus, and B. wanghaotingi, in Southern China and Northern Myanmar are particularly obscure. Despite the extensively overlapping distributions for the three species, only B. multicinctus has been documented in Hong Kong. Following genetic analyses, we suggest that both B. multincinctus and B. wanghaotingi occur in Hong Kong. However, our morphological examinations are overall inconclusive in distinguishing the two species. With potential interspecific antivenin differences, the new identification of B. wanghaotingi in Hong Kong is of important medical interest. We recommend further ecological, taxonomic, and behavioural studies be conducted to properly distinguish B. multincinctus and B. wanghaotingi in the region.

Therapeutic Himalayan herbs: Folklore uses, bioactive phytochemicals, and biological activities of medicinal orchids used by Nomads

Natural products have bioactive properties which have been exploited for human and animal use for hundreds of years. Orchids are one of the largest, diverse, and most evolved groups of plants within monocot angiosperms. Different species under this category have been recognized as the most threatened plants due to poor seed germination, the need for endophytic mycorrhizal partners, and habitat destructions coupled with climate change. The majority of orchid taxa are known to have therapeutic potential due to the presence of bioactive substances, such as alkaloids, bibenzyls, phenanthrenes, phenanthrenequinones, glycosides, carbohydrates, flavonoids, and stilbenoids. In this study, twenty-eight indigenous Himalayan orchids were documented from six Himalayan states and one union territory of India viz ., Acampe ochracea, Aerides odorata, A. multiflora, Anoectochilus setaceus , Arundina graminifolia , Bulbophyllum odoratissimum , Coelogyne corymbosa , C. punctulata , Crepidium acuminatum , Cymbidium aloifolium , C. elegans , Dendrobium densiflorum , D. fimbriatum , D. fugax , D. nobile , Eulophia graminea , Habenaria dentata , H. marginata , Herminium lanceum , Liparis nervosa , Papilionanthe teres , Phaius tankervilleae , Pholidota imbricata , P. pallida , Porpax muscicola , Rhynchostylis retusa , Vanda coerulea and V. cristata familiar to nomadic tribes for use as medicine in their daily life. Data collected on species identity and nomenclature, local names, uses, bioactive constituents, pharmacological bioactivities, and phenology are presented. These findings will help in preserving Himalayan traditional knowledge, conservation of endangered plants, and research and development associated with wild orchids or similar taxa elsewhere in the globe.

Eponyms associated with the nomenclature of the recent species of rhinoceros

Since 1758, a total of 16 eponyms have been described to honour explorers and taxonomists for the recent species of rhinoceros. This paper presents short biographies and the circumstances of the description of these names used in zoological nomenclature. The name blythii was named after Edward Blyth (1810–1873), brucii after James Bruce (1730–1794), burchellii after William John Burchell (1781–1863), Campbell’s rhinoceros after John Campbell (1766–1840), camperis, camperii, camperi after Petrus Camper (1722–1789), cottoni after Percy Horace Gordon Powell-Cotton (1866–1940), crossii after Edward Cross (1774–1854), floweri after William Henry Flower (1831–1899), gordoni after Robert Jacob Gordon (1743–1795), harrissoni after Tom Harrisson (1911–1976), holmwoodi after Frederick Holmwood (d.1896), jamrachi after William Jamrach (1842–1923), michaeli after Michael Grzimek (1934–1959), and oswelli after William Cotton Oswell (1818–1893). Résumé Depuis 1758, un total de 16 éponymes ont étés décrits pour honorer les explorateurs et les taxonomistes des espèces récentes de rhinocéros. Cet article présente de brèves biographies et les circonstances liées à la description de ces noms utilisés dans la nomenclature zoologique. Le nom blythii a été nommé d'après Edward Blyth (1810–1873), brucii d’après James Bruce (1730–1794), burchellii d’après William John Burchell (1781–1863), le rhinocéros de Campbell d’après John Campbell (1766–1840), camperis, camperii, camperi d'après Petrus Camper (1722–1789), cottoni d'après Percy Horace Gordon Powell-Cotton (1866–1940), crossii d'après Edward Cross (1774–1854), floweri d'après William Henry Flower (1831–1899), gordoni d'après Robert Jacob Gordon (1743–1795), harrissoni d’après Tom Harrisson (1911–1976), holmwoodi d’après Frederick Holmwood (décédé en 1896), jamrachi après William Jamrach (1842–1923), michaeli d’après Michael Grzimek (1934–1959) et oswelli d’après William Cotton Oswell (1818–1893).

Genomic constitution, allopolyploidy, and evolutionary proposal for Cynodon Rich. based on GISH.

Polyploidy is the main mechanism for chromosome number variation in Cynodon. Taxonomic boundaries are difficult to define and, although phylogenetic studies indicate that some species are closely related, the degree of genomic similarity remains unknown. Furthermore, the Cynodon species classification as auto or allopolyploids is still controversial. Thus, this study aimed to investigate the genomic constitution in diploid and polyploid species using different approaches of genomic in situ hybridization (GISH). To better understand the hybridization events, we also investigated the occurrence of unreduced gametes in C. dactylon diploid pollen grains. We suggest a genomic nomenclature of diploid species as DD, D1D1, and D2D2 for C. dactylon, C. incompletus, and C. nlemfuensis, and DDD2D2 and DD2D1D1 for the segmental allotetraploids of Cynodon dactylon and C. transvaalensis, respectively. Furthermore, an evolutionary proposal was built based on our results and previous data from other studies, showing possible crosses that may have occurred between Cynodon species.

Elucidating the nomenclature and taxonomy of Phalaena euphemia Stoll, 1781, the type species of the genus Heraclia Hbner, [1820] (Lepidoptera, Noctuidae, Agaristinae).

The genus Heraclia (Lepidoptera, Noctuidae, Agaristinae) and the species involved in the confused nomenclature and taxonomy of the type species, Phalaena euphemia Stoll, 1781 are investigated. The rediscovery of the type specimen of Noctua geryon Fabricius, 1781, a taxon that had previously been treated as the senior synonym of euphemia, justified the revival of the latter from synonymy with the former. The type material of euphemia could not be traced and a neotype is designated to fix the published name to a physical specimen. In addition to detailed diagnoses and re-descriptions, the revised taxonomy of Heraclia euphemia and Heraclia geryon is provided and the following new synonymies are proposed: Eusemia pallida Walker, 1854 and Eusemia niveosparsa Westwood, 1881 are synonymised with H. geryon and Eusemia nugatrix Westwood, 1881 is synonymised with H. euphemia. Distributional data for each of the species are presented.

A 2021 taxonomy update for the family Smacoviridae.

The family Smacoviridae (order Cremevirales, class Arfiviricetes, phylum Cressdnaviricota) is comprised of viruses with small circular single-stranded DNA genomes of ~2.3-3 kb in length that have primarily been identified in fecal sample of various animals. Smacovirus genomes carry two genes in ambisense orientation encoding a capsid protein and a rolling-circle replication initiation protein, respectively. We have revised the taxonomy of the family by assigning 138 new genomic sequences deposited in GenBank to already established taxa as well as 41 new species and six new genera. Furthermore, we have adopted binomial species nomenclature, conforming to the "Genus + freeform epithet" format for all 84 species from 12 genera. The updated Smacoviridae taxonomy presented in this article has been ratified by the International Committee on Taxonomy of Viruses (ICTV).

Isolation and genetic characterization of a relapsing fever spirochete isolated from Ornithodoros puertoricensis collected in central Panama.

Tick-borne relapsing fever (TBRF) spirochetes are likely an overlooked cause of disease in Latin America. In Panama, the pathogens were first reported to cause human disease in the early 1900s. Recent collections of Ornithodoros puertoricensis from human dwellings in Panama prompted our interest to determine whether spirochetes still circulate in the country. Ornithodoros puertoricensis ticks were collected at field sites around the City of Panama. In the laboratory, the ticks were determined to be infected with TBRF spirochetes by transmission to mice, and we report the laboratory isolation and genetic characterization of a species of TBRF spirochete from Panama. Since this was the first isolation of a species of TBRF spirochete from Central America, we propose to designate the bacteria as Borrelia puertoricensis sp. nov. This is consistent with TBRF spirochete species nomenclature from North America that are designated after their tick vector. These findings warrant further investigations to assess the threat B. puertoricensis sp. nov. may impose on human health.

Revision of the South American catfish genus Hypophthalmus (Siluriformes, Pimelodidae) with descriptions of two new species from the Amazon and Orinoco Basins

The pimelodid genus Hypophthalmus is a small group of pelagic and planktivorous catfishes that are abundant and variously distributed in the lowland river basins of the Amazon, Parnaíba, Orinoco, Guianas and Paraná. Since their earliest published descriptions, commencing over 190 years ago with H. edentatus Spix and Agassiz 1829, the taxonomy and nomenclature of Hypophthalmus species have been confused and unresolved. In this study, four of the six available species names are validated and two new species are described. Newly discovered characters of the vertebral column, circumoral barbels, pelvic fins, and lateralis sensory canals provide strong support and diagnostics for species and species-groups. A key to species, anatomical descriptions, notes on identification of small juveniles and phylogenetic interrelationships are included. A lectotype is designated for Hypophthalmus marginatus and nominal Hypophthalmus longifilis, respectively.

The extremely large chloroplast genome of the green alga Haematococcus pluvialis: Genome structure, and comparative analysis

Astaxanthin is arguably nature's most potent antioxidant, powerful to prevent free radical damage and oxidative stress. The microalga Haematococcus pluvialis seems to accumulate the highest levels of astaxanthin in nature and thus is currently the primary industrial source for natural astaxanthin production. The accumulation happens under photooxidative stress to quench radical damage from the photosynthesis, which is considered as one of the main reasons why chloroplast genomes are usually kept the small size and high guanine-cytosine (GC) content. We hypothesize that the outstanding astaxanthin production of the species may reflect its chloroplast genome features. In this study, the complete chloroplast genome of H. pluvialis FACHB-712 was sequenced and investigated. The genome is large, comprising 1.35 Mbp with 83 genes. However, the GC content is counterintuitively as high as 50.1%. The genome shows slight phylogenetic distance and genome structural differences in comparison with that of H. lacustris, whose species nomenclature is confusing and controversial. Moreover, a possible correlation between its powerful antioxidant capacity and the large chloroplast genome maintenance was further investigated. Strains of Chlorophyta and several strains with chloroplast genomes size of more than 500 kbp were used for comparative analysis. The evolutionary mechanism for the large chloroplast genome and and the contribution of non-coding region ratio and GC content to genome amplification is discussed.Large genomes may be associated with harsh habitats, and increased GC content may be used to increase stability.

Expanding the Knowledge on the Skillful Yeast Cyberlindnera jadinii.

Cyberlindnera jadinii is widely used as a source of single-cell protein and is known for its ability to synthesize a great variety of valuable compounds for the food and pharmaceutical industries. Its capacity to produce compounds such as food additives, supplements, and organic acids, among other fine chemicals, has turned it into an attractive microorganism in the biotechnology field. In this review, we performed a robust phylogenetic analysis using the core proteome of C. jadinii and other fungal species, from Asco- to Basidiomycota, to elucidate the evolutionary roots of this species. In addition, we report the evolution of this species nomenclature over-time and the existence of a teleomorph (C. jadinii) and anamorph state (Candida utilis) and summarize the current nomenclature of most common strains. Finally, we highlight relevant traits of its physiology, the solute membrane transporters so far characterized, as well as the molecular tools currently available for its genomic manipulation. The emerging applications of this yeast reinforce its potential in the white biotechnology sector. Nonetheless, it is necessary to expand the knowledge on its metabolism, regulatory networks, and transport mechanisms, as well as to develop more robust genetic manipulation systems and synthetic biology tools to promote the full exploitation of C. jadinii.

A comment on “An evolutionary system of mineralogy: Proposal for a classification of planetary materials based on natural kind clustering”

Abstract The classification and nomenclature of mineral species is regulated by the Commission on New Minerals, Nomenclature and Classification of the International Mineralogical Association (IMACNMNC). This mineral species classification is necessary for Earth Sciences, as minerals constitute most planetary and interstellar materials. Hazen (2019) has proposed a classification of minerals and other Earth and planetary materials according to “natural clustering.” Although this classification is complementary to the IMA-CNMNC mineral classification and is described as such, there are some unjustified criticisms and factual errors in the comparison of the two schemes. It is the intent of the present comment to (1) clarify the use of classification schemes for Earth and planetary materials, and (2) counter erroneous criticisms or statements about the current IMA-CNMNC system of approving proposals for new mineral species and classifications.

Ecological and faunal analysis of dragonflies (Odonata) of suborders Zygoptera, Caloptera in Republic of Ingushetia

In this work, we adhere to the systematics proposed by the school of odonatologists B.F.Belyshev, that is, the order is subdivided into three suborders: Anizoptera, Zygoptera and Caloptera. In this article, we first characterize the suborders Zygoptera, Caloptera. The article provides a systematic composition and an overview of taxa common in the RI. [one]. On the basis of literature sources, brief characteristics of suborders, families and genera are given, and the problems of taxonomy and nomenclature of individual species and basic information on the distribution of taxa found in the study area are discussed. Analysis of the existing stream of literary information on dragonflies indicates that there are still problems, the solution of which requires close attention. First of all, this is the lack of research on the Caucasian regional odonatofaunas.

Reply to “A comment on ‘An evolutionary system of mineralogy: Proposal for a classification of planetary materials based on natural kind clustering’”

AbstractI welcome the “Comment” from Hatert et al. (2021) related to the proposal for an “Evolutionary system of mineralogy” (Hazen 2019) and thank them for their historically informed, conceptually nuanced, and consistently constructive contribution. They offer corrections related to two facets of my paper that seemed unfairly to criticize aspects of the International Mineralogical Association's Commission on New Minerals, Nomenclature and Classification (IMA-CNMNC) protocols for classifying minerals.First, they note an unfortunate inferred ambivalence with respect to the relationship between the IMA system and the new evolutionary system. If I was once ambivalent, that view has changed. Having spent the past two years in an ongoing effort to develop this new historical approach, I am struck every day by the power of the IMA-CNMNC system of species classification and nomenclature, which is fundamental and indispensable to the science of mineralogy. As Hatert et al. suggest, any new approach to organizing natural solids, including one focused on planetary evolution, must rest on the foundation provided by the IMA-CNMNC and its many volunteers who selflessly bring order to the mineral kingdom. In the best scenario, the evolutionary system may one day emerge as one of several useful approaches that complement and amplify but in no way replace this core IMA-CNMNC foundation, as clearly stated in the abstract of Hazen (2019).Second, Hatert et al. (2021) offer corrections regarding the IMA-CNMNC approach to classification, in particular a mischaracterization of the formal process to incorporate amorphous phases, poorly crystalline materials, and loosely defined “mineraloids.” I am grateful for the clarifications, as well as the implication that IMA protocols may facilitate the embrace of additional such phases in the future.Finally, I welcome the chance to explore further the emerging concept of “natural kinds” as applied to the mineral kingdom. Here, our thoughts differ. I suggest that minerals, considered in their information-rich, idiosyncratic, paragenetic contexts (in contrast to IMA-CNMNC species), have the potential to represent quintessential examples of “natural kinds.” Furthermore, when viewed in their evolutionary context, minerals offer an intriguing opportunity to expand the concept of “historical natural kinds” beyond its present limited and, at times, controversial use in biology, into the realm of the co-evolving geosphere and biosphere.

A review of the genus Strophidon (Anguilliformes: Muraenidae), with description of a new species.

Strophidon McClelland is a muraenid genus with characteristic appearance of a very elongated body, a large mouth cleft and anteriorly placed eyes. The nomenclature and taxonomic history of species within Strophidon are contentious and its members are easily misidentified. In the present study, species of the genus Strophidon are revised based on morphological and molecular data, and five species are considered valid, including S. dawydoffi Prokofiev, S. dorsalis (Seale), S. sathete (Hamilton), S. ui Tanaka and a new species, S. tetraporus. Strophidon tetraporus sp. nov. is described based on 15 specimens from Indonesia, the Philippines, Taiwan and Vietnam with the unique characteristic of the constant presence of the fourth infraorbital pore among species of Strophidon. The intraspecific variation of vertebral formula within S. dorsalis is discussed based on molecular data. Muraena macrurus Bleeker and Thyrsoidea longissima Kaup are synonyms of S. sathete that can be distinguished from the most similar congener S. ui by a longer tail, smaller eyes and more inner maxillary and inner dentary teeth. A key to identify species of Strophidon is provided. The distribution and maximum size of each species are also re-evaluated.

Cyto- and myeloarchitectural brain atlas of the pale spear-nosed bat (Phyllostomus discolor) in CT Aided Stereotaxic Coordinates

The pale spear-nosed bat Phyllostomus discolor, a microchiropteran bat, is well established as an animal model for research on the auditory system, echolocation and social communication of species-specific vocalizations. We have created a brain atlas of Phyllostomus discolor that provides high-quality histological material for identification of brain structures in reliable stereotaxic coordinates to strengthen neurobiological studies of this key species. The new atlas combines high-resolution images of frontal sections alternately stained for cell bodies (Nissl) and myelinated fibers (Gallyas) at 49 rostrocaudal levels, at intervals of 350 µm. To facilitate comparisons with other species, brain structures were named according to the widely accepted Paxinos nomenclature and previous neuroanatomical studies of other bat species. Outlines of auditory cortical fields, as defined in earlier studies, were mapped onto atlas sections and onto the brain surface, together with the architectonic subdivisions of the neocortex. X-ray computerized tomography (CT) of the bat’s head was used to establish the relationship between coordinates of brain structures and the skull. We used profile lines and the occipital crest as skull landmarks to line up skull and brain in standard atlas coordinates. An easily reproducible protocol allows sectioning of experimental brains in the standard frontal plane of the atlas. An electronic version of the atlas plates and supplementary material is available from https://doi.org/10.12751/g-node.8bbcxy

Additional Species Records and Nomenclature Updates of Butterflies from a Threatened Coastal Habitat in Southern Sonora, Mexico

Additional Species Records and Nomenclature Updates of Butterflies from a Threatened Coastal Habitat in Southern Sonora, Mexico

<p><strong>Friedrich Welwitsch and his overlooked contributions to the <em>Flora of Tropical Africa</em>, with a discussion of the names of <em>Kalanchoe</em> (Crassulaceae subfam. Kalanchooideae) that should be ascribed to Welwitsch alone</strong></p>

Although it is widely assumed that Friedrich Welwitsch, who collected about 10,000 specimens in Angola during a seven-year period in the mid-1800s, only proposed names that were validly published by other authors in the Flora of Tropical Africa (FTA), he also provided Latin descriptions that were attached to the specimens. These descriptions were translated into English and used in FTA. Welwitsch was therefore the only author of those names. As a case study, the nomenclature of new species published in the FTA in the genus Kalanchoe (Crassulaceae subfam. Kalanchooideae) is presented. When all the internal evidence in the relevant FTA volume is taken into account, the authorship of all the Kalanchoe species names, bar one, K. welwitschii, which was published by Britten exclusively, is Welwitsch only, and not “Welwitsch ex Britten” or “Welwitsch ex Oliver” as usually cited. Kalanchoe coccinea and K. brachyloba, whose distributions extend beyond Angola, have type localities in that country, and were also based on Welwitsch’s descriptions. An itinerary of Welwitsch’s Angolan expedition and maps showing the areas where he collected in the country are provided. Type localities from where Welwitsch collected the Kalanchoe species published in FTA are placed on the map. The typification of seven Kalanchoe names is clarified, some through correcting previous designations and, where required, second-step lectotypifications.

Ethnobotanical knowledge of home garden plant species and its effect on home garden plant diversity in Thies region of Senegal

Home gardens are the first source of immediate contact between people and plants since the gardens are within homesteads. Most home garden studies in Senegal concentrate on food security and economic benefits; no research has been carried out on the social and ecological contexts of home gardening in Senegal. It is therefore necessary to evaluate the way people interact with the home garden plants and how such an interface influences plant diversity. The objective of this study is to evaluate the ethnobotanical knowledge associated to home garden plants and its effect on plant diversity conservation in home gardens. A sample of 30 home gardens was selected from the three main departments of the region and was used to collect plant species data. Data were collected from informants who were selected basing on recommendations from village leaders. Techniques used were plant inventory, participatory observations and individual interviews. Species nomenclature was based on Senegal analytical flora and the world plant list; comparison of effect between different variables was analyzed in analytical software R using simple linear regression analysis. A total of 96 plant species were identified; all species were found to be useful plants divided into eight functional groups. Fifty-four percent (54%) were food species, 40% medicinal, 32% ornamental, 14% commercial, 7% fodder, 4% sacred, 4% ceremonial and 3% cosmetic. Citrus limon was the most frequent (80%) and preferred species in the home gardens. Food plant species are the most diversified, abundant and rich use category. There is a relationship between uses of species and species diversity (P value < 0.001). Species diversity in the home gardens increases as the spectrum of use increases; thus, species with more than one use were highly diversified; people prefer multipurpose species for multiple benefits. This study expresses home gardens as diversified agroecosystems for sustainable biodiversity conservation of useful plant species.

Disappearing apple snails (Caenogastropoda: Ampullariidae) of Thailand: a comprehensive update of their taxonomic status and distribution

ABSTRACT Ampullariidae include the largest of all freshwater snails and are of ecological, evolutionary and anthropogenic importance in Southeast Asia (SEA). Native ampullariids belonging to the genus Pila face various threats but are understudied, with their species taxonomy being confused and data on their distributions being scarce. We provide a comprehensive update on the nomenclature, status and distribution of Pila species in Thailand, based on DNA barcoding and geometric morphometric analysis of recently collected material. We confirm that at least five Pila species are extant in Thailand: Pila virescens, P. celebensis, P. turbinis, P. gracilis and P. pesmei. Pila celebensis, which has distinctive egg masses among all the known Southeast Asian Pila, appears to be sister to a clade comprising other SEA and some African Pila. Our results suggest that Pila may have dispersed into SEA on at least two separate occasions. Two singletons collected from northern and eastern Thailand may constitute separate species, but this requires further study. Intraspecific diversity of the mitochondrial cytochrome c oxidase subunit I gene was relatively high for P. celebensis, P. gracilis and P. pesmei (maximum uncorrected p-distances varied from 7% to 9%), and may include cryptic species. Conversely, P. virescens showed low intraspecific p-distances (c. 0%) among clades collected from different localities. This strongly suggests that introductions by humans may be the major cause of this pattern, and our own observations—we found that this species is being cultured and is commonly sold in markets for human consumption—are consistent with this. Pila turbinis was the rarest species, with live snails being collected from only two localities. Throughout Thailand, invasive confamilial Pomacea species appear to be replacing native Pila species, particularly in the Chao Phraya basin. While Thai Pila exhibit surprisingly high genetic diversity, with cryptic species likely being present, widespread invasive snails pose a major threat to their survival and urgent conservation action is needed.

Molecular characterization of Pseudomonas from Agaricus bisporus caps reveal novel blotch pathogens in Western Europe

BackgroundBacterial blotch is a group of economically important diseases affecting the cultivation of common button mushroom, Agaricus bisporus. Despite being studied for more than a century, the identity and nomenclature of blotch-causing Pseudomonas species is still unclear. This study aims to molecularly characterize the phylogenetic and phenotypic diversity of blotch pathogens in Western Europe.MethodsIn this study, blotched mushrooms were sampled from farms across the Netherlands, United Kingdom and Belgium. Bacteria were isolated from symptomatic cap tissue and tested in pathogenicity assays on fresh caps and in pots. Whole genome sequences of pathogenic and non-pathogenic isolates were used to establish phylogeny via multi-locus sequence alignment (MLSA), average nucleotide identity (ANI) and in-silico DNA:DNA hybridization (DDH) analyses.ResultsThe known pathogens “Pseudomonas gingeri”, P. tolaasii, “P. reactans” and P. costantinii were recovered from blotched mushroom caps. Seven novel pathogens were also identified, namely, P. yamanorum, P. edaphica, P. salomonii and strains that clustered with Pseudomonas sp. NC02 in one genomic species, and three non-pseudomonads, i.e. Serratia liquefaciens, S. proteamaculans and a Pantoea sp. Insights on the pathogenicity and symptom severity of these blotch pathogens were also generated.ConclusionA detailed overview of genetic and regional diversity and the virulence of blotch pathogens in Western Europe, was obtained via the phylogenetic and phenotypic analyses. This information has implications in the study of symptomatic disease expression, development of diagnostic tools and design of localized strategies for disease management.