Sphenophyllum miravallis Vetter and Bowmanites cupulatus sp.n. from the “Illinger Flözzone” (“Heusweiler Schichten”, Lower Stephanian, Saar Basin, German Federal Republic)

This paper deals with a detailed study of Sphenophyllum miravallis Vetter, a member of the “Sphenophyllum thonii group”. New material from the Reisbach colliery, working the “Illinger Flözzone” of the “Heusweiler Schichten” (Lower Stephanian, Saar Basin, German Federal Republic), is described morphologically and anatomically, and the species is discussed. The new material enlarges the known range of variability of the normal aspect of the foliage, i.e. the foliage of the thinner branches. Thicker stems with their aberrant polymorphous foliage, and cellular details, are described for the first time. An emended diagnosis is given. Comparisons with other species are made.

The new species Bowmanites cupulatus is introduced to accommodate fructufications most probably belonging to Sphenophyllum miravallis.

S. crenulatum Knight ex Wagner is considered to be a heterotypic synonym of S. miravallis, the latter name having priority.     

Should taxon names be explicitly defined?

Overviews are provided for traditional and phylogenetic nomenclature. In traditional nomenclature, a name is provided with a type and a rank. In the rankless phylogenetic nomenclature, a taxon name is provided with an explicit phylogenetic definition, which attaches the name to a clade. Linnaeus’s approach to nomenclature is also reviewed, and it is shown that, although the current system of nomenclature does use some Linnaean conventions (e.g., certain rank-denoting terms, binary nomenclature), it is actually quite different from Linnaean nomenclature. The primary differences between traditional and phylogenetic nomenclature are reviewed. In phylogenetic nomenclature, names are provided with explicit phylogenetic definitions, whereas in traditional nomenclature names are not explicitly defined. In phylogenetic nomenclature, a name remains attached to a clade regardless of how future changes in phylogeny alter the clade’s content; in traditional nomenclature a name is not “married” to any particular clade. In traditional nomenclature, names must be assigned ranks (an admittedly arbitrary process), whereas in phylogenetic nomenclature there are no formal ranks. Therefore, in phylogenetic nomenclature, the name itself conveys no hierarchical information, and the name conveys nothing regarding set exclusivity. It is concluded that the current system is better able to handle new and unexpected changes in ideas about taxonomic relationships. This greater flexibility, coupled with the greater information content that the names themselves (i.e., when used outside the context of a given taxonomy or phytogeny) provide, makes the current system better designed for use by all users of taxon names.     

关于规范涉及喜马拉雅山的物种中文命名的建议

虽然国际生物科学联合会已经明确了“学名”的法定地位,但在实际工作中仍然离不开中文名的使用。本文通过对以“himalaya”拉丁化命名的6个属、402个物种,以及涉及“喜马拉雅山”的1个属、37个种中文名的分析,发现有3个属和35个物种中文名命名不规范。这些命名中不恰当的简化违反了地名法定原则、史料记载和行业惯例,由此提出修订不规范命名的建议。     

Correct identification of species makes the amoebozoan rRNA tree congruent with morphology for the order Leptomyxida Page 1987; with description of Acramoeba dendroida n. g., n. sp., originally misidentified as 'Gephyramoeba sp.'

Morphological identification of protists remains an expert task, especially for little known and poorly described species. Culture collections normally accept organisms under the name provided by depositors and are not responsible for identification. Uncritical acceptance of these names by molecular phylogeneticists may result in serious errors of interpretation of phylogenetic trees based on DNA sequences, making them appear more incongruent with morphology than they really are. Several cases of misidentification in a major culture collection have recently been reported. Here we provide evidence for misidentifications of two more gymnamoebae. The first concerns “Gephyramoeba sp.” ATCC 50654; it is not Gephyramoeba, a leptomyxid with lobose pseudopods, but a hitherto undescribed branching amoeba with fine, filamentous subpseudopods named here Acramoeba dendroida gen. et sp. nov. We also sequenced 18S rRNA of Page's strain of Rhizamoeba saxonica (CCAP 1570/2) and show that it is the most deeply branching leptomyxid and is not phylogenetically close to ‘Rhizamoeba saxonica’ ATCC 50742, which was misidentified. Correcting these misidentifications improves the congruence between morphological diversity of Amoebozoa and their rRNA-based phylogenies, both for Leptomyxida and for the Acramoeba part of the tree. On morphological grounds we transfer Gephyramoebidae from Varipodida back to Leptomyxida and remove Flamella from Leptomyxida; sequences are needed to confirm these two revisions.     

Cochliopodium barki n. sp. (Rhizopoda, Himatismenida) re-isolated from soil 30 years after its initial description

A strain of Cochliopodium isolated from grassland soil at Sourhope Research Station (Scotland, UK) was found to be identical to the strain “Cochliopodium sp.2” studied by Bark in 1973. We name it Cochliopodium barki. It belongs to a group of species (comprising also C. minus and Cochliopodium sp. “NYS strain”) with very similar scale pattern.     

Molecular phylogeny and taxonomic revision of Chlamydomonas (Chlorophyta). I. Emendation of Chlamydomonas Ehrenberg and Chloromonas Gobi, and description of Oogamochlamys gen. nov. and Lobochlamys gen. nov

The genus Chlamydomonas (including Chloromonas) is one of the largest green algal genera comprising more than 600 species. To initiate a comprehensive analysis of the phylogeny and systematics of the genus, we determined nuclear-encoded SSU rRNA sequences from 32 strains of Chlamydomonas, Chloromonas and Chlorogonium with emphasis on oogamous taxa and related strains, and incorporated these into global molecular phylogenetic analyses of 132 strains of Chlorophyceae. In addition, we studied the morphology and reproduction of oogamous and related strains by light microscopy. We recognize and designate 18 monophyletic lineages (clades) within the Chlorophyceae, 11 of which are confined to the CW (basal bodies displaced clockwise) subgroup. The majority of clades recognized within the Chlorophyceae do not correspond to any of the traditional classification systems, which are still largely based on the organization level. Strains assigned to Chlamydomonas and Chloromonas were found in seven different clades confirming the polyphyly of the two genera as presently conceived. To initiate the taxonomic revision of Chlamydomonas, C. reinhardtii is proposed as the conserved type of the genus. In consequence, species in clades other than the clade containing C. reinhardtii must be transferred to other genera, a process initiated in this contribution. The oogamous strains studied represent a monophyletic lineage, which is described as Oogamochlamys gen. nov. comprising three species (O. gigantea, O. zimbabwiensis and O. ettlii spec. nov.). The sister clade to Oogamochlamys consists of isogamous strains characterized by chloroplasts with incisions and is described as Lobochlamys gen. nov. with two species (L. culleus and L. segnis). Another clade is characterized by asteroid or perforated, parietal chloroplasts and contains the type species of Chloromonas (C. reticulata). Thus, the polyphyletic Chloromonas (traditionally defined as “Chlamydomonas without pyrenoids”) can be legitimized as a monophyletic genus by restriction to this clade and is here emended on the basis of chloroplast characters (the clade contains strains with or without pyrenoids thus rejecting the character “absence of pyrenoids”).     

与蝉花有关的虫草菌生物多样性的研究I：文献考证

蝉花是我国重要药用真菌,但长期以来其名称特别是学名的使用一直混乱。本文从古代医药典籍记载确认,“蝉花”是历史最久、使用最广的中名,对于其他中名具有优先权。其学名Isaria cicadae系Miquel（1838）根据巴西标本命名,但模式标本已失,原描述文字及插图均极其简单,与蝉花形态差异较大。其有性型迄今未发现,曾先后被认为是小蝉草Ophiocordyceps sobolifera和大蝉草Tolypocladium dujiaolongae (=Cordyceps cicadae Shing)。本文根据文献考证澄清了国内外关于小蝉草和大蝉草的误用,分析了长期以来大量日本文献中的命名混乱对我国认知蝉花的影响,并质疑I. cicadae在中国及其他地区的分布,提出它是一复合种,因此蝉花的分类地位及学名需要进一步研究。     

Toward an integrated system of clade names

Although the proposition that higher taxa should correspond to clades is widely accepted, current nomenclature does not distinguish clearly between different clades in nested series. In particular, the same name is often applied to a total clade, its crown clade, and clades originating with various nodes, branches, and apomorphies in between. An integrated system of clade names is described based on categories of clades defined with respect to lineages that have survived to the present time. In this system, the most widely known names are applied to crown clades, the names of total clades are formed by adding a standard prefix to the names of the corresponding crowns, and the names of apomorphy clades describe the specific apomorphies with which they originated. Relative to traditional approaches, this integrated approach to naming clades is both more precise concerning the associations of names with particular clades and more efficient with regard to the cognitive effort required to recognize the names of corresponding crown and total clades. It also seems preferable to five alternatives that could be used to make the same distinctions. The integrated system of clade names has several advantages, including the facilitation of communication among biologists who study distantly related clades, promoting a broader conceptualization of the origins of distinctive clades of extant organisms and emphasizing the continuous nature of evolution.     

Ceci n'est pas une pipe: names, clades and phylogenetic nomenclature

An introduction is provided to the literature and to issues relating to phylogenetic nomenclature and the PhyloCode, together with a critique of the current Linnaean system of nomenclature. The Linnaean nomenclature fixes taxon names with types, and associates the names with ranks (genus, family, etc.). In phylogenetic nomenclature, names are instead defined with reference to cladistic relationships, and the names are not associated with ranks. We argue that taxon names under the Linnaean system are unclear in meaning and provide unstable group–name associations, notwithstanding whether or not there are agreements on relationships. Furthermore, the Linnaean rank assignments lack justification and invite unwarranted comparisons across taxa. On the contrary, the intention of taxon names in phylogenetic nomenclature is clear and stable, and the application of the names will be unambiguous under any given cladistic hypothesis. The extension of the names reflects current knowledge of relationships, and will shift as new hypotheses are forwarded. The extension of phylogenetic names is, therefore, clear but is associated to (and thus dependent upon) cladistic hypotheses. Stability in content can be maximized with carefully formulated name definitions. A phylogenetic nomenclature will shift the focus from discussions of taxon names towards the understanding of relationships. Also, we contend that species should not be recognized as taxonomic units. The term ‘species’ is ambiguous, it mixes several distinct classes of entities, and there is a large gap between most of the actual concepts and the evidence available to identify the entities. Instead, we argue that only clades should be recognized. Among these, it is useful to tag the smallest named clades, which all represent non-overlapping groups. Such taxa  – LITUs (Least Inclusive Taxonomic Units) – are distinguished from more inclusive clades by being spelled with lower-case initial letter. In contrast to species, LITUs are conceptually straightforward and are, like other clades, identified by apomorphies.     

Species names in phylogenetic nomenclature

Linnaean binomial nomenclature is logically incompatible with the phylogenetic nomenclature of de Queiroz and Gauthier (1992, Annu. Rev. Ecol. Syst. 23:449-480): The former is based on the concept of genus, thus making this rank mandatory, while the latter is based on phylogenetic definitions and requires the abandonment of mandatory ranks. Thus, if species are to receive names under phylogenetic nomenclature, a different method must be devised to name them. Here, 13 methods for naming species in the context of phylogenetic nomenclature are contrasted with each other and with Linnaean binomials. A fundamental dichotomy among the proposed methods distinguishes those that retain the entire binomial of a preexisting species name from those that retain only the specific epithet. Other relevant issues include the stability, uniqueness, and ease of pronunciation of species names; their capacity to convey phylogenetic information; and the distinguishability of species names that are governed by a code of phylogenetic nomenclature both from clade names and from species names governed by the current codes. No method is ideal. Each has advantages and drawbacks, and preference for one option over another will be influenced by one's evaluation of the relative importance of the pros and cons for each. Moreover, sometimes the same feature is viewed as an advantage by some and a drawback by others. Nevertheless, all of the proposed methods for naming species in the context of phylogenetic nomenclature provide names that are more stable than Linnaean binomials.     

The species of Hymenoptera described by Linnaeus in the genera Sphex, Chrysis, Vespa, Apis and Mutilla

Data are presented on the type-material representing the species described by Linnaeus in his genera Sphex, Chrysis, Vespa, Apis and Mutilla , The names here considered total 158; six are currently applied in the Hymenoptera Parasitica. Of the balance of 147, three are emendations and five are unavailable homonyms or names proposed in the synonymy of other species. Fifteen Linnaean names are here placed as synonyms. One name is attributed to an author other than Linnaeus, and live names remain species incertae sedis. The remainder, 118, are applied as valid names in die Hymenoptera Aculeata. Holotype specimens in London, Uppsala or Stockholm represent 60 names; 55 names are based on lectotype specimens of which 49 are here designated, two by other authors. One name is represented by a neotype specimen in Lund, and one by a lectotype figure. One non-aculeate species is based on syntypes. Specimens appear to be lost with respect to 25 names; three specimens in Uppsala may be the holotypes of a further three species.
Eight new combinations are made, and twelve new synonyms established; three further new combinations and three further new synonymies are suggested. A systematically arranged summary of species treated and of nomenclatural changes made is given. Nomenclatural changes affecting non-Linnaean names are included where relevant; lectotypes are designated for two non-Linnaean species.     

English names for a world list of mammals, exemplified by species of Indochina

1. The lack of a globally accepted list of English‐language names for mammal species leads to various problems stemming from the reduced ability to communicate unambiguously. This impacts directly on their conservation. We use the larger mammals of Indochina to exemplify the use of an explicit set of principles designed to provide each species with a unique and non‐misleading (or at least minimally so) English name. 2. For most species, a suitable name is already in use, sometimes generally so. For species for which multiple names are in use, standardization would consist of adopting the most suitable name. Only for a very few species are all extant names so unsuitable that a neologism should be coined. One species, Panthera pardus, presents potentially insoluble problems. 3. Name standardization among the world's birds has generated some controversy, but this has not led to abandonment of the process. Much can be learned by those developing a similar process for mammals, through studying the bird‐naming process. Progress can be advanced by detractors indicating whether they oppose standardization per se, the principles used or the names resulting from application of the principles. Also, proponents of standardization should always emphasize that the purpose of the process is to produce a list available for those who want to use it, not to produce a binding selection that must be used in all circumstances.     

Current usage of nomenclature for parasitic diseases, with special reference to those involving arthropods

Terminological confusion has been aggravated by efforts to develop a standardized nomenclature for parasitic diseases (SNOPAD) arising from the proposal by Kassai et al., 1988) for a standardized nomenclature of animal diseases (SNOAPAD). To restabilize international nomenclature of parasitic diseases it is recommended that, whenever appropriate, names should follow the 'International Nomenclature of Diseases' (IND) compiled by the Council for International Organizations for Medical Sciences (CIOMS/WHO, 1987). For diseases not included in IND, familiarity should guide the choice of name: traditional English language names of diseases should be preferred, e.g. 'malaria', 'scabies' or, for parasitic diseases having no traditional name, the taxonomic name of the causative organism should be applied, e.g. 'Brugia timori microfilaraemia'; 'Plasmodium malariae infection'; 'Simulium allergy'--instead of the generic derivatives proposed by SNOPAD, i.e. brugiosis, plasmodiosis and simuliidosis, respectively. For names of new diseases or those rarely mentioned, the suffix -osis would normally take precedence. Generally, the name of choice for any disease in any language should be the vernacular term, with commonest English usage preferred for international communication, and publications should include synonyms in the list of keywords.     

Taxonomy, distribution and nomenclature of three confused broad-leaved Potamogeton species occurring in Africa and on surrounding islands

A taxonomic revision of broad-leaved Potamogeton species ascribed to the ' P. schweinfurthii–thunbergii complex' occurring in Africa and on surrounding islands is presented. Three species, P. nodosus , P. richardii and P. schweinfurthii , are recognized in the African mainland. The widespread species P. nodosus has been widely overlooked in sub-Saharan Africa. It is recorded here for the first time from eight countries of tropical and southern Africa and from six surrounding islands. The distribution of P. richardii is critically revised and the species is recorded for the first time from Cameroon, Swaziland and Madagascar. P. schweinfurthii is recorded for the first time from Algeria, Tunisia, Burkina Faso and Niger. The nomenclature of all three species is revised. Lectotypes are designated for six names. All original material of the name P. thunbergii Cham. et Schltdl. actually belongs to P. nodosus Poir. The correct name for the East and southern African species called ' P. thunbergii ' is P. richardii Solms. The lectotype of P. schweinfurthii designated by Dandy proved to be P. nodosus . A new type is therefore proposed for the species generally named P. schweinfurthii and the name itself is proposed for conservation. The morphology and stem anatomy of P. nodosus , P. richardii and P. schweinfurthii are described. In spite of some overlaps in the morphological variation in their vegetative characters, a detailed analysis of the variation patterns and instructions for reliable identification are given. The distributions of all three species are described, based solely on reliably identified specimens, many of which were also examined anatomically. Distribution maps are provided.  © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society , 2005, 148 , 329–357.     

Description of two new species of Bodinia, a new genus incertae sedis in Argestidae Por, 1986 (Copepoda, Harpacticoida), with reflections on argestid colonization of the Great Meteor Seamount plateau

The present paper focuses on the results of taxonomic, faunistic and chorologic investigations on Argestidae Por, 1986 (Copepoda, Harpacticoida). All argestid species collected during the cruise M42/3 of RV “Meteor” (1998) are new to science. In the present contribution, two species are described and united within Bodinia gen. nov.: Bodinia meteorensis sp. nov. and Bodinia peterrummi sp. nov. The new genus is placed as incertae sedis in Argestidae in light of uncertainty concerning the phylogenetic relations within this group and even its status as a monophylum. The question is discussed how members of Argestidae, previously seen as a deep-sea taxon, may have colonized the shallow-water habitat of the Great Meteor Seamount plateau.     

Review of ‘The Plant List,a working list of all plant species’

The Plant List ( http://www.theplantlist.org/ ) is an on‐line database of plant names that aims to be comprehensive for all described plant species. Version 1 of The Plant List includes 1 040 426 plant name records, of which 298 900 are accepted names. The Plant List is the product of a consortium of the Royal Botanic Gardens, Kew, and the Missouri Botanical Garden. In this review, I evaluate the use of this plant taxonomic database for plant ecologists. The web interface of The Plant List allows a quick search for species names and corresponding synonyms. Moreover, users are able to download search or browse results to compile a customized checklist of plant names. The combination of a straightforward web design and the possibility to download search results provides a valuable resource of plant nomenclature information for a wide range of plant ecologists.     

Leucobacter chromiireducens sp. nov, and Leucobacter aridicollis sp. nov., two new species isolated from a chromium contaminated environment

Two strains designated strains L-1^T and L-9^T were isolated from activated sludge of a treatment plant that receives wastewater from the tannery industry contaminated with chromium. Phylogenetic analysis showed that the organisms represented two new species of the genus Leucobacter. Strains L-1^T and L-9^T could be distinguished from the type strain of L. komagatae and from the type strain of “L. albus” by the B-type peptidoglycan composition, fatty acid composition, several phenotypic and physiological characteristics. The major fatty acids of the organisms were iso- and anteiso-branched C15:0 and C17:0, straight-chain C16:0 was also found in relatively high proportions. The organisms were halotolerant, grew in medium containing 9% NaCl, and all strains, including the type strain of L. komagatae grew in medium containing 5 mM Cr(VI). On the basis of the distinct peptidoglycan composition, 16S ribosomal DNA sequence analysis, percentage of DNA-DNA reassociation values, and phenotypic characteristics we are of the opinion that strain L-1^T represents a new species of the genus Leucobacter for which we propose the name Leucobacter chromiireducens and that strain L-9^T represents an additional new species of the same genus for which we propose the name Leucobacter aridicollis.     

The family of Deg/HtrA proteases in plants

ABSTRACT: BACKGROUND: The Deg/HtrA family of ATP-independent serine endopeptidases is present in nearly all organisms from bacteria to human and vascular plants. In recent years, multiple deg/htrA protease genes were identified in various plant genomes. During genome annotations most proteases were named according to the order of discovery, hence the same names were sometimes given to different types of Deg/HtrA enzymes in different plant species. This can easily lead to false inference of individual protease functions based solely on a shared name. Therefore, the existing names and classification of these proteolytic enzymes does not meet our current needs and a phylogeny-based standardized nomenclature is required. RESULTS: Using phylogenetic and domain arrangement analysis, we improved the nomenclature of the Deg/HtrA protease family, standardized protease names based on their well-established nomenclature in Arabidopsis thaliana, and clarified the evolutionary relationship between orthologous enzymes from various photosynthetic organisms across several divergent systematic groups, including dicots, a monocot, a moss and a green alga. Furthermore, we identified a "core set" of eight proteases shared by all organisms examined here that might provide all the proteolytic potential of Deg/HtrA proteases necessary for a hypothetical plant cell. CONCLUSIONS: In our proposed nomenclature, the evolutionarily closest orthologs have the same protease name, simplifying scientific communication when comparing different plant species and allowing for more reliable inference of protease functions. Further, we proposed that the high number of Deg/HtrA proteases in plants is mainly due to gene duplications unique to the respective organism.