Nomenclatural Implications Research Articles

Phylogenetic relationships of the gecko genus Carinatogecko (Reptilia: Gekkonidae)

The gecko genus Carinatogecko comprises two species endemic to the foothills of the Zagros Mountains, in Iran and Iraq. Both species are poorly known and to date they are known only from very few records. The phylogenetic affiliation of the genus has been only hypothesized. The aim of this study was to clarify the phylogenetic relationships of the genus by analyzing partial sequences of the mitochondrial 12S rRNA and cytochrome b genes. All phylogenetic analyses performed support placing the genus Carinatogecko within the genus Mediodactylus. Taxonomic relevance of both species of the genus Carinatogecko based on morphological characters is discussed along with nomenclatural implications of our findings.

The presence of accessory cusps in chimpanzee lower molars is consistent with a patterning cascade model of development

Tooth crown morphology is of primary importance in fossil primate systematics and understanding the developmental basis of its variation facilitates phenotypic analyses of fossil teeth. Lower molars of species in the chimp/human clade (including fossil hominins) possess between four and seven cusps and this variability has been implicated in alpha taxonomy and phylogenetic systematics. What is known about the developmental basis of variation in cusp number - based primarily on experimental studies of rodent molars - suggests that cusps form under a morphodynamic, patterning cascade model involving the iterative formation of enamel knots. In this study we test whether variation in cusp 6 (C6) presence in common chimpanzee and bonobo lower molars (n = 55) is consistent with predictions derived from the patterning cascade model. Using microcomputed tomography we imaged the enamel-dentine junction of lower molars and used geometric morphometrics to examine shape variation in the molar crown correlated with variation in C6 presence (in particular the size and spacing of the dentine horns). Results indicate that C6 presence is consistent with predictions of a patterning cascade model, with larger molars exhibiting a higher frequency of C6 and with the location and size of later-forming cusps correlated with C6 variation. These results demonstrate that a patterning cascade model is appropriate for interpreting cusp variation in Pan and have implications for cusp nomenclature and the use of accessory cusp morphology in primate systematics.

English

An overview of the debate surrounding the correct generic name for the triggerplants (Stylidium Sw., Candollea Labill., Ventenatia Sm.; Stylidiaceae) is provided. The authorship of Stylidium and the four species published in Willdenow’s Species Plantarum in 1805 is here attributed to Swartz in Willdenow rather than Swartz ex Willdenow, since Willdenow clearly credits these taxa to Swartz; however, the month of publication of these taxa could not be verified. The nomenclatural implications of a publication date subsequent to that of Candollea, also published in 1805, are discussed. Stylidium graminifolium Sw., previously thought to be based on a gathering by Banks and Solander, is shown to be based on a collection by Dr John White, first Surgeon-General of New South Wales. The type of S. lineare Sw. was similarly collected by White. A revised type citation and synonymy are provided for both species and lectotypes selected for Stylidium graminifolium var. angustifolium Mildbr., Ventenatia major Sm. and V. minor Sm.

Type specimens, samples of live individuals and the Galapagos Pink Land Iguana

The nomenclatural implications of Gentile & Snell (2009)'s innovations in the designation of a type specimen - that is sampled and tagged but not killed - are discussed. The paper also responds to Nemésio (2009)'s criticism of Donegan (2008), where I argued that descriptions based on samples of live individuals are valid. I also discuss whether recent descriptions of such a nature involve a different degree of scientific rigour to other descriptions.

Lectotypifications and notes on the application of names of Hieracium sect. Hieracium, sect. Bifida and sect. Vulgata (Asteraceae) based on material from the province of Dalarna, central Sweden

Lectotypes are designated for 174 names of taxa described based on material from the Swedish province of Dalarna and accepted to belong to Hieracium sect. Hieracium, sect. Bifida and sect. Vulgata. The taxonomic and nomenclatural implications, i.e. taxonomic synonyms and infraspecific taxa not worthy of taxonomic recognition, of the lectotypifications are discussed. Three new combinations, H. mundulifolium (Johanss.) T. Tyler, H. oligasterum (Johanss. & Sam.) T. Tyler and H. transtrandense T. Tyler, are proposed to accommodate the infraspecific taxa H. gilvocaniceps Johanss. var. mundulifolium Johanss., H. expallidiforme (Dahlst. ex. Stenstr.) Dahlst. var. oligasterum Johanss. & Sam. and H. insuccatum Johanss. var. occidentale Johanss. & Sam. respectively, when treated at the rank of species.

Correcting the type designation of Pterocarpus tessmannii Harms (Leguminosae–Papilionoideae)

A lectotype for Pterocarpus tessmannii Harms (Leguminosae–Papilionoideae) is selected and its nomenclature implications are discussed.

Vertex Spirals in Fullerenes and Their Implications for Nomenclature of Fullerene Derivatives

The IUPAC nomenclature of fullerene derivatives is based on the vertex spiral, but not all fullerenes possess one. There are 1495 isomers with <or=20 vertices (66 isolated-pentagon isomers with <or=150 vertices) that are vertex-aspiral, but only four for which all vertex spiral starts succeed. Vertex-aspiral trivalent polyhedra are common (40 190 with <or=24 vertices); infinite series include truncates of all trivalents larger than the tetrahedron. An alternative and readily automated breadth-first-search numbering scheme is proposed to deal with all trivalent polyhedra including fullerenes and incidentally to give robust, efficient determination of the automorphism/point group. For fullerenes, the new scheme has two clear advantages over the vertex spiral nomenclature: it is exception-free, removing the need for complex prescriptions to deal with exceptional cases, and it is mathematically simpler in that the numbering can be found in linear rather than quadratic time (as all canonical numberings for a fullerene begin on a pentagon).

JOURNAL POLICY ON NAMES OF AEDINE MOSQUITO GENERA AND SUBGENERA

The International Code of Zoological Nomenclature exists to promote stability and universality of scientific names in taxonomy, using the Linnean binomial system (genus and species), to ensure that the valid name of each species is distinct within each unique genus, according to the rules of priority. In the context of biosystematics, the code does not restrict freedom of taxonomic thought or action. Through the code, nomenclature shows the rank accorded to any formal group of animals (e.g., family or tribe, genus or subgenus, species or subspecies) leaving ample scope for informal categories such as species complexes, phylogenetic clades, and other groups. All classifications and reclassifications above the species level depend on subjective interpretation of taxonomic evidence, so uniformity is arrived at through consensus among systematists, and eventually adopted by the rest of the scientific community. Reclassifications that result in changing the names of common pests and vectors, for which there is extensive older literature, inevitably create considerable confusion among teachers, students, and researchers, with communication difficulties and financial implications for republishing educational materials, keys, catalogs, and management of databases. When reinterpreting the relationships between species and groups of applied importance, systematists have responsibility to limit the impact on nomenclature. Such caution was not exercised when the majority of known species and subgenera of Aedes mosquitoes were transferred to the restored genus Ochlerotatus based on taxonomic characters that few other workers have examined. 1 Many investigators adopted the new name combinations without fully understanding the reasons. Savage and Strickman 2 gave a comprehensive argument against splitting Ochlerotatus from Aedes, whereas Black 3 defended this step. The latest proposal by Reinert and others 4 to elevate dozens of additional subgenera of Aedini to generic status creates a further dilemma for journal editors and authors. Mosquito systematists and cladists remain divided on the appropriateness of these changes. Anyone can join the debate at http://wrbu.si.edu/forums. Meanwhile, authors should be aware of the current editorial policy of the American Journal of Tropical Medicine and Hygiene (AJTMH) on this fluid issue. AJTMH* takes the position that more research (including molecular evidence) and interpretation are needed to develop a consensus on the reclassification of Aedini proposed by Reinert 1 and Reinert and others. 4 In particular, the nomenclatural implications need to be separated from their cladistic analyses. Accordingly, AJTMH encourages authors dealing with aedine mosquitoes to maintain usage of the traditional names (http://www.mosquitocatalog.org/main.asp), except when the author has taxonomic reasons for not doing so. AJTMH also will permit authors to adopt the newly proposed classification of Aedini (with 46 genera recognized by Reinert and others 4 ) if they are convinced of the case, e.g., for elevation of any particular genus. In such cases, authors are asked to include the previous binomial combination when the species is first mentioned in the text of any submitted paper, as in the following examples: Stegomyia albopicta ( Aedes albopictus, see Reinert and others 4 ), Ochlerotatus triseriatus ( Aedes triseriatus, see Reinert 1 ).

Taxonomic and Nomenclatural Implications of Phylogenetic Studies of the Bryaceae Based on Molecular Data and Morphology

The taxonomic and nomenclatural implications of phylogenetic studies of the Bryaceae are presented. Bryum algovicum Müll. Hal., B. archangelicum Müll. Hal., B. capillare Hedw., B. bimum (Schreb.) Turner, B. cyclophyllum (Schwägr.) Bruch & Schimp., B. donianum Grev., B. lisae De Not., B. meesioides Kindb., B. orthothecium Card. & Broth., B. pallens Sw., B. pallescens Schwägr., B. purpurascens (R. Br.) Bruch & Schimp., B. uliginosum (Brid.) Bruch & Schimp., and B. wrightii Sull. are transferred to Plagiobryum Lindb. Brachymenium acuminatum Harv., B. philonotula Broth., and B. preissianum Hampe (A. Jaeger) are transferred to Bryum Hedw. Finally, the genus Imbribryum is described comprising B. alpinum With, B. blandum Hook. f. & Wilson, and Bryum muehlenbeckii Bruch & Schimp.

The myxomycete genus Schenella: morphological and DNA sequence evidence for synonymy with the gasteromycete genus Pyrenogaster

The genus Schenella has proven difficult to classify since its description as a new genus in 1911. Macbride placed it with the Myxomycetes but it was unclear with which myxomycete, if any, it should be grouped. Recent identification of abundant samples of Schenella has aided a re-evaluation of its classification as a myxomycete. Morphological evidence based on light and scanning electron microscopy of recently collected specimens and on the type specimen of Macbride suggested that it might be synonymous with the gasteromycete Pyrenogaster. Analysis of DNA sequences from freshly isolated samples indicates that the genus Schenella is related closely to an anciently diverged, monophyletic group of fungi that includes several gasteromycete genera, among them Geastrum, Sphaerobolus and Pseudocolus. Comparisons of the morphology and DNA sequences of authentically identified specimens of Pyrenogaster atrogleba indicate that it is synonymous with Schenella simplex. The nomenclatural implications of this discovery are discussed.

The myxomycete genus Schenella: morphological and DNA sequence evidence for synonymy with the gasteromycete genus Pyrenogaster

The genus Schenella has proven difficult to classify since its description as a new genus in 1911. Macbride placed it with the Myxomycetes but it was unclear with which myxomycete, if any, it should be grouped. Recent identification of abundant samples of Schenella has aided a re-evaluation of its classification as a myxomycete. Morphological evidence based on light and scanning electron microscopy of recently collected specimens and on the type specimen of Macbride suggested that it might be synonymous with the gasteromycete Pyrenogaster Analysis of DNA sequences from freshly isolated samples indicates that the genus Schenella is related closely to an anciently diverged, monophyletic group of fungi that includes several gasteromycete genera, among them Geastrum, Sphaerobolus and Pseudocolus. Comparisons of the morphology and DNA sequences of authentically identified specimens of Pyrenogaster atrogleba indicate that it is synonymous with Schenella simplex. The nomenclatural implications of this discovery are discussed.

Bilimbia (Lichenes) resurrected

Bilimbia [Rheede] Rchb. (Oxalidaceae) is not validly published, whereby Bilimbia De Not. (Lichenes) is not a later homonym and must replace Myxobilimbia Hafellner. In an Appendix, the nomenclatural implications are acted upon: Bilimbia De Not. is re-instated and the new combination Bilimbia lobulata (Sommerf.) Hafellner &amp; Coppins is made.

Nomenclature and typification in the genus Usnea (lichenized Ascomycetes)—I. Usnea rigida

Recent work has led to the discovery that Usnea rigida (Acharius) Motyka has been mis-interpreted by many authors and that the nomenclatural implications of its re-interpretation affect the use of some other names. The following errors are corrected: U. rigida (Acharius) Motyka should be cited as U. rigida Motyka and is not synonymous with U. florida var. rigida Acharius; U. florida var. rigida is lectotypified and placed in synonymy with U. florida (L.) Wigg.; U. rigida Vainio has priority over U. rigida Motyka; U. welwitschiana Motyka is regarded as a superfluous name. U. quasirigida, nom. nov., is introduced for U. rigida Motyka (non U. rigida Vainio).

Genetic identification and characterization of a novel virus related to human hepatitis E virus from chickens with hepatitis-splenomegaly syndrome in the United States.

Hepatitis-splenomegaly (HS) syndrome is an emerging disease in chickens in North America; the cause of this disease is unknown. In this study, the genetic identification and characterization of a novel virus related to human hepatitis E virus (HEV) isolated from bile samples of chickens with HS syndrome is reported. Based upon the similar genomic organization and significant sequence identity of this virus with HEV, the virus has been tentatively named avian HEV in order to distinguish it from human and swine HEV. Electron microscopy revealed that avian HEV is a non-enveloped virus particle of 30-35 nm in diameter. The sequence of the 3' half of the viral genome ( approximately 4 kb) was determined. Sequence analyses revealed that this genomic region contains the complete 3' non-coding region, the complete genes from open reading frames (ORFs) 2 and 3, the complete RNA-dependent RNA polymerase (RdRp) gene and a partial helicase gene from ORF 1. The helicase gene is the most conserved gene between avian HEV and other HEV strains, displaying 58-61% aa and 57-60% nt sequence identities. The RdRp gene of avian HEV shares 47-50% aa and 52-53% nt sequence identities and the putative capsid gene (ORF 2) of avian HEV shares 48-49% aa and 48-51% nt sequence identities with the corresponding regions of other known HEV strains. Phylogenetic analysis indicates that avian HEV is genetically related to, but distinct from, other known HEV strains. This discovery has important implications for HEV animal models, nomenclature and natural history.

CYP9E2, CYP4C21 and related pseudogenes from German cockroaches, Blattella germanica: implications for molecular evolution, expression studies and nomenclature of P450s

The cDNAs of two novel P450s (CYP9E2 and CYP4C21) were isolated from German cockroaches, Blattella germanica. Both CYP9E2 and CYP4C21 are typical microsomal P450s and their deduced amino acid sequences share a number of common characteristics with other members of the P450 superfamily. Northern blot analyses using a CYP9E2 or CYP4C21 probe showed that ‘CYP9E2’ and ‘CYP4C21’ were expressed at all life stages. Two pseudogenes related to CYP9E2 and three pseudogenes related to CYP4C21 were also isolated. These represent the first P450 pseudogenes from an insect other than Drosophila melanogaster. The relative number of P450 pseudogenes in B. germanica is apparently higher than in D. melanogaster. The implications of these results for the molecular evolution, expression studies and nomenclature of P450s are discussed.

Relationships within the Proteobacteria of plant pathogenic Acidovorax species and subspecies, Burkholderia species, and Herbaspirillum rubrisubalbicans by sequence analysis of 16S rDNA, numerical analysis and determinative tests.

Sequence data for 16S rDNA of the type strains of Acidovorax avenae subsp. avenae, A. avenae subsp. cattleyae, A. avenae subsp. citrulli, A. konjaci and Herbaspirillum rubrisubalbicans were compared with GenBank library accessions of Burkholderia spp., Comamonas sp., Ralstonia solanacearum and Variovorax sp. Maximum Parsimony analysis produced two clusters: 1. Acidovorax spp., Comamonas sp., and Variovorax sp. (all in the Comamonadaceae), and 2. Burkholderia spp., Ralstonia solanacearum, and Herbaspirillum rubrisubalbicans. Maximum Likelihood analysis produced only one cluster (of the Comamonadaceae). Using nutritional and laboratory tests, all Acidovorax spp., Burkholderia spp., and Herbaspirillum rubrisubalbicans were discriminated in distinct clusters at the species level, and could be identified by selected determinative tests. There were no phenotypic tests constituted as a circumscription of the genera and which permitted the allocation of strains to genera. Strain identification as species allowed allocation to genera only by inference. The nomenclatural implications of these data are discussed.

Criteria for the Classification of Hormone Receptors with Implications for Nomenclature

Criteria for the Classification of Hormone Receptors with Implications for Nomenclature

Regional Correlations in the South Caspian Sea - Implications for Stratigraphic Nomenclature: ABSTRACT

Regional Correlations in the South Caspian Sea - Implications for Stratigraphic Nomenclature Detailed sequence boundary correlations in the South Caspian sea have led to a better understanding of the relationships between stratigraphic units identified in wells throughout the basin. With the aid of synthetic seismograms, used to tie the logs to the seismic data, lithologic units have been identified seismically and have been mapped across the basin. The synthetic seismograms were created from pseudo-sonic logs which were transformed from resistivity logs with the Faust equation. Checkshots and VSP surveys supplied the velocity control. The sequence boundary correlations revealed substantial facies changes across the basin and led to the creation of a new stratigraphic correlation chart which relates local formation names to their time correlative boundaries. A recognition of these facies changes has led to a better understanding of the lithologic relationships within the basin, the depositional history of the basin, and the source and distribution of potential reservoir sands. Previous well log correlations, made primarily by matching tops of sand and shale sequences, frequently crossed sequence boundaries mapped from seismic data. Lithologic units, deposited under similar geologic conditions, often looked the same but were not time equivalent. Seismic sequence analysesmore » have shown that tectonic movements, as evidenced by rising domes, created barriers to sediment distribution and led to pronounced thickness changes on opposite sides of a high. New log correlations, incorporating these concepts, are helping to unravel the complex structural and stratigraphic history of the South Caspian Sea.« less

Factors to consider in the naming of a G protein-coupled receptor subtype.

Receptors that mediate their effects through G proteins are predicted to have a seven transmembrane domain architecture. The last few years have seen a remarkable increase in the cloning of members of this superfamily leading to the identification of many more receptors than previously thought to exist on the basis of differences in agonist and antagonist specificities. This has important implications for nomenclature and classification, especially in view of the difficulty in relating receptors identified through cloning techniques to endogenously expressed receptors. Receptor cloning has also identified important differences in receptors between species raising the question as to whether these should be considered as species homologues or distinct subtypes. It is also becoming increasingly apparent that the pharmacology of this superfamily of receptors is influenced by the nature of the G protein present in the host cell and by alternative splicing of the receptor. The rapid pace of developments in this area necessitate the need for a regular publication summarizing recent developments. In the future, the cloning of G protein-coupled receptors will enable rationalization of the naming of individual receptor subtypes and identification of their interrelationships.

South African fungi 3: A reinvestigation of Pearson’s Lepiota types

Descriptions are given of Lepiota canescens, L. cristato-cystidiata, L. cutifracta, L. fustiformis, L. truncata and L. umbrino-zonata. Lepiota canescens is reduced to synonymy under L. truncata. The diagnosis of L. fustiformis is shown to be based on two different taxa and the nomenclatural implications are discussed. The following new combinations are proposed: Leucoagaricus cristato-cystidiatus, Leucocoprinus truncatus, L. umbrino-zonatus. Lepiota praeclara and L.roseoiescensboth belong in Amanita.