Phylogenetic relationships of the subclass Peritrichia (Oligohymenophorea, Ciliophora) inferred from small subunit rRNA gene sequences

The phylogenetic relationships among peritrichs remain unresolved. In this study, the complete small subunit rRNA (SSrRNA) gene sequences of seven species (Epistylis galea, Campanella umbellaria, Carchesium polypinum, Zoothamnium arbuscula, Vaginicola crystallina, Ophrydium versatile, and Opercularia microdiscum) were determined. Trees were constructed using distance-matrix, maximum-likelihood and maximum-parsimony methods, all of which strongly supported the monophyly of the subclass Peritrichia. Within the peritrichs, 1) E. galea grouped with Opercularia microdiscum and Campanella umbellaria but not the other Epistylis species, which indicates that the genus Epistylis might not be monophyletic; 2) the topological position of Carchesium and Campanella suggested that Carchesium should be placed in the family Zoothamniidae, or be elevated to a higher taxonomic rank, and that Campanella should be independent of the family Epistylididae, and probably be given a new rank; and 3) Opisthonecta grouped strongly with Astylozoon, which suggested that Opisthonecta species were not the ancestors of the stalked peritrichs.     

Overview of the taxonomy of zooxanthellate Scleractinia

Coral taxonomy has entered a historical phase where nomenclatorial uncertainty is rapidly increasing. The fundamental cause is mandatory adherence to historical monographs that lack essential information of all sorts, and also to type specimens, if they exist at all, that are commonly unrecognizable fragments or are uncharacteristic of the species they are believed to represent. Historical problems, including incorrect subsequent type species designations, also create uncertainty for many well‐established genera. The advent of in situ studies in the 1970s revealed these issues; now molecular technology is again changing the taxonomic landscape. The competing methodologies involved must be seen in context if they are to avoid becoming an additional basis for continuing nomenclatorial instability. To prevent this happening, the International Commission on Zoological Nomenclature (ICZN) will need to focus on rules that consolidate well‐established nomenclature and allow for the designation of new type specimens that are unambiguous, and which include both skeletal material and soft tissue for molecular study. Taxonomic and biogeographic findings have now become linked, with molecular methodologies providing the capacity to re‐visit past taxonomic decisions, and to extend both taxonomy and biogeography into the realm of evolutionary theory. It is proposed that most species will ultimately be seen as operational taxonomic units that are human rather than natural constructs, which in consequence will always have fuzzy morphological, genetic, and distribution boundaries. The pathway ahead calls for the integration of morphological and molecular taxonomies, and for website delivery of information that crosses current discipline boundaries. © 2013 The Author. Zoological Journal of the Linnean Society published by John Wiley & Sons Ltd. on behalf of The Linnean Society of London     

A molecular phylogenetic investigation of Opisthonecta and related genera (Ciliophora, Peritrichia, Sessilida)

The gene encoding 18S small subunit ribosomal RNA (ssu rRNA) was sequenced in the sessiline peritrichs Opisthonecta minima and Opisthonecta matiensis, whose free-swimming, paedomorphic trophonts resemble telotrochs. Using these new sequences, phylogenetic trees were constructed with four different methods to test a previously published association between Opisthonecta henneguyi and members of the families Vorticellidae and Astylozoidae. All trees had similar topologies, with O. minima, O. henneguyi, Vorticella microstoma, and Astylozoon enriquesi forming a well-supported, certainly monophyletic clade. On the basis of genetic evidence, genera of the families Opisthonectidae and Astylozoidae are assigned to the family Vorticellidae, which already includes some species with free-swimming morphotypes. The ssu rRNA sequence of O. matiensis places it in the family Epistylididae; its taxonomic revision will be left to another group of authors. A close association of Ophrydium versatile with members of the family Vorticellidae was confirmed, casting doubt on the validity of the family Ophrydiidae. Epistylis galea, Campanella umbellaria, and Opercularia microdiscum are confirmed as comprising an extremely distinct, monophyletic, but morphologically heterogeneous clade that is basal to other clades of sessiline peritrichs.     

Type specimens of Mitridae (Mollusca:Gastropoda) described by Linnaeus in the genera Voluta, Buccinum and Bulla between 1758 and 1771

From the 16 species of Mitridae described by Linnaeus between the years 1758-71 11 species are considered valid and available for taxonomic use; four specific names have been suppressed by the International Commission on Zoological Nomenclature for taxonomic usage (1968). One specific name, i.e. Voluta mitra episcopalis Linnaeus, has appeared in various combinations in malacological literature over the years. From the style of listing in the 10th edition of the Systerna Naturae , it is evident that 'episcopalis' has to be treated as of infraspecific rank; there is no evidence that 'episcopalis' is even a valid subspecies of Voluta mitra.
Three holotypes and five lectotypes designated in this paper are extant in the Linnaean collection; illustrations representing three Linnaean species have been selected as lectotypes.     

利用三种分子标记研究缘毛类纤毛虫的系统发育地位

为了探讨缘毛类纤毛虫的系统发育地位 ,利用RAPD方法得到了 9种缘毛类纤毛虫、 1种四膜虫和1种喇叭虫的 3个随机引物的电泳带谱 ;测定了 7种缘毛类纤毛虫rRNA基因中的间隔区 1(ITS1)和小亚基核糖体核糖核酸 (SSrRNA)基因序列 ,并构建了相应的系统树。在比较和分析RAPD、ITS1和SSrRNA基因序列在缘毛类纤毛虫系统发育研究中的适用范围的基础上 ,以SSrRNA基因序列为分子标记研究了缘毛类纤毛虫系统发育地位 ,结果表明 :①缘毛亚纲是单系的 ,作为寡膜纲中一个亚纲的分类地位是合理的 ;②缘毛类纤毛虫可能是寡膜纲中较高等的一个类群。     

Edmund Keffer Kline 1894-1976

It is with deep regret that the friends of Dr. E. K. Kline learned of his death on January 26th, 1976. Dr. Kline served with the Biological Stain Commission for many years, joining the Board of Trustees as representative of the American Public Health Association shortly after the reorganization of the Commission during the latter stages of World War II. Dr. Kline served as Vice-president of the Commission from 1963 to 1966, and as President from 1966 to 1969. His warm good nature and sound judgement combined effectively to help advance the goals of the Commission throughout his period of service, and his absence will be keenly felt.     

Tsukamurella spumae sp. nov., a novel actinomycete associated with foaming in activated sludge plants

A polyphasic taxonomic study was undertaken to establish the taxonomic position of six representative strains isolated from activated sewage sludge foam. The organisms were found to have chemical and morphological properties consistent with their assignment to the genus Tsukamurella. DNA:DNA relatedness studies showed that five out of the six isolates formed a distinct genomic species, the remaining strain was most closely associated with this taxon. The five isolates had a unique phenotypic profile that served to distinguish them from representatives of the validly described species of Tsukamurella. The combination of the genotypic and phenotypic data indicated that the five strains should be classified as a new species in the genus Tsukamurella. The name proposed for this taxon is Tsukamurella spumae, the type strain is N1171T (= DSM 44.113T = NCIMB 13947T). It was also shown that some of the reference strains were misclassified as Tsukamurella paurometabola.     

Implementation of the 1990 recommendations of ICRP in the countries of the European community

The International Commission on Radiological Protection (ICRP) has published new Recommendations in ICRP Publication 60. These 1990 Recommendations provide a System of Radiological Protection that takes account of the most recent information on the effects on health of exposure to ionising radiation and trends in the setting of safety standards. Within the European Community the Recommendations fo the ICRP are implemented through a Euratom Directive which is binding on member states, a draft of which has been accepted by the Article 31 Group and must eventually be ratified by the Council of Ministers. It is expected that the new directive will broadly endorse the principles of protection given in the 1990 Recommendations together with the dose limits for both workers and members of the public. There are likely to be some modifications to the 1990 Recommendations that are mainly related to their practical application. As it will be some time before the directive is incorporated into national regulations, a number of member states have taken independent initiatives. The development of dose constraints for occupational, medical and public exposure is being seen by national organisations in many countries as a significant new approach to improving standards of radiation protection.     

Phylogenetic relationships within the class Oligohymenophorea,phylum Cilophora,inferred from the complete small subunit rRNA gene sequences ofColpidium campylum,Glaucoma chattoni,andOpisthonecta henneguyi

Summary Phylogenetic relationships within the class Oligohymenophorea, phylum Ciliophora, were investigated by determining the complete small subunit rRNA (SSrRNA) gene sequences for the hymenostomesColpidium campylum, Glaucoma chattoni, and the peritrichOpisthonecta henneguyi. The affiliations of the oligohymenophoreans were assessed using both distance matrix (DM) and maximum parsimony (MP) analyses. Variations do exist in the phylogenies created by the two methods. However, the basic tree topologies are consistent. In both the DM and MP analyses the hymenostomes (C. campylum, G. chattoni, and the tetrahymenas) all form a very tight group associated with the peritrichO. henneguyi. TheTetrahymena lineage was monophyletic whereasColpidium andGlaucoma were more closely related to each other than either was to the tetrahymenas. The monophyly of the genusTetrahymena in the present analysis supports the phylogenies determined from morphological data and molecular sequence data from the histone H3II/H4II region of the genome. The perplexing and controversial phylogenetic position of the peritrichs is once again depicted in the present analysis. The distinctiveness of the peritrichOpisthonecta from both hymenostome and nassophorean ciliates based on evolutionary distances suggests that the elevation of the peritrichs to a higher taxonomic rank should be reconsidered.     

Double skeletons of silicoflagellates: Their reciprocal position and taxonomical and paleobiological values

The author addresses some problems concerning the double skeletons of silicoflagellates using examples from the Middle Miocene of Romania in conjunction with examples published in the recent literature. The main problem concerns the cause of the reciprocal position of the two individuals in double skeletons, which may occur either with the basal spines and corners of the basal rings of the two specimens aligned, or rotated from one another under different angles. Since the basal ring of the daughter skeleton must be in close proximity to that of the mother skeleton during its skeletogenesis, the main cause of rotation or non-rotation is attributed to the presence or absence of sustaining spines and their position on skeleton, namely beneath the struts or migrated onto the basal ring. A secondary cause is the position of basal spines relative to the plane of the basal ring. An approximate value of the angle of rotation of the basal rings is 180° per number of sustaining spines or struts. Species without sustaining spines, or with these spines migrated clockwise beneath the basal ring, are not rotated. In addition, species without sustaining spines are rotated when some basal spines or all are tilted under the plane of the basal ring. Cretaceous species without a basal ring are also rotated during skeletogenesis under angles depending on number of struts according to the same formula. The importance of this study is multiple: it indicates that silicoflagellates multiply asexually, it may solve some taxonomic problems, and it provides a mechanism in which new morphologies can appear suddenly, without intermediaries. From paleobiological point of view, this study provides an explanation of why in fossil materials, the position of the daughter skeleton with respect to the mother one was in many cases different from that of living species. A short taxonomic appendix is included with a brief discussion of the taxonomic problems of some genera and species mentioned in this article.     

Comparative anatomy of nine species of the genus Rhododendron from Qinghai Plateau and their systematic position

Anatomical characteristics of the wood, the branchlets and the leaf blades of nine representative species of Rhododendron on Qinghai plateau have been examined in order to explore their taxonomic position. On the basis of vessel figures in growth rings, the wood of Rhododendron can be divided into two divisions, namely, semi-ring pore and scattered pore wood. Because of the differences of the wood ray-structure and the glandular hairs on the branchlets andthe leaf blades, the latter can be further classified into two subdivisions.     

Zoological nomenclature in the digital era

Creation and use of the scientific names of animals are ruled by the International Code of Zoological Nomenclature. Until recently, publication of new names in a work produced with ink on paper was required for their availability. A long awaited amendment to the Code issued in September 2012 by the International Commission on Zoological Nomenclature now allows publication of new names in online-only works, provided that the latter are registered with ZooBank, the Official Register of Animal Names. With this amendment, the rules of zoological nomenclature have been aligned with the opportunities (and needs) of our digital era. However, possible causes for nomenclatural instability remain. These could be completely removed if the Code-compliant publication of new names will be identified with their online registration, under suitable technological and formal (legal) conditions. Future developments of the ZooBank may provide the tool required to make this definitive leap ahead in zoological nomenclature.     

Reevaluation of the phylogenetic relationship between mobilid and sessilid peritrichs (Ciliophora, Oligohymenophorea) based on small subunit rRNA genes sequences

Based on morphological characters, peritrich ciliates (Class Olygohymenophorea, Subclass Peritrichia) have been subdivided into the Orders Sessilida and Mobilida. Molecular phylogenetic studies on peritrichs have been restricted to members of the Order Sessilida. In order to shed more light into the evolutionary relationships within peritrichs, the complete small subunit rRNA (SSU rRNA) sequences of four mobilid species, Trichodina nobilis, Trichodina heterodentata, Trichodina reticulata, and Trichodinella myakkae were used to construct phylogenetic trees using maximum parsimony, neighbor joining, and Bayesian analyses. Whatever phylogenetic method used, the peritrichs did not constitute a monophyletic group: mobilid and sessilid species did not cluster together. Similarity in morphology but difference in molecular data led us to suggest that the oral structures of peritrichs are the result of evolutionary convergence. In addition, Trichodina reticulata, a Trichodina species with granules in the center of the adhesive disc, branched separately from its congeners, Trichodina nobilis and Trichodina heterodentata, trichodinids without such granules. This indicates that granules in the adhesive disc might be a phylogenetic character of high importance within the Family Trichodinidae.     

What can genome-scale metabolic network reconstructions do for prokaryotic systematics?

It has recently been proposed that in addition to Nomenclature, Classification and Identification, Comprehending Microbial Diversity may be considered as the fourth tenet of microbial systematics [Staley JT (2010) The Bulletin of BISMiS, 1(1): 1–5]. As this fourth goal implies a fundamental understanding of microbial speciation, this perspective article argues that translation of bacterial genome sequences into metabolic features may contribute to the development of modern polyphasic taxonomic approaches. Genome-scale metabolic network reconstructions (GSMRs), which are the result of computationally predicted and experimentally confirmed stoichiometric matrices incorporating all enzyme and metabolite components encoded by a genome sequence, provide a platform that can illustrate bacterial speciation. As the topology and the composition of GSMRs are expected to be the result of adaptive evolution, the features of these networks may provide the prokaryotic taxonomist with novel tools for reaching the fourth tenet of microbial systematics. Through selected examples from the Actinobacteria, which have been inferred from GSMRs and experimentally confirmed after phenotypic characterisation, it will be shown that this level of information can be incorporated into modern polyphasic taxonomic approaches. In conclusion, three specific examples are illustrated to show how GSMRs will revolutionize prokaryotic systematics, as has previously occurred in many other fields of microbiology.     

Chemicals in aroids: a survey, including new results for polyhydroxy alkaloids and alkylresorcinols

The Araceae is a large, mainly tropical family, many members of which contain bioactive substances which are often either toxic or irritating. Inflorescences frequently emit strong fragrances. The active compounds have not been adequately determined nor is the chemotaxonomy of the family very well known, except for one major study of flavonoids. Two groups of compounds of known bioactivity—alkylresorcinols and nitrogenous sugar analogues—have been sought in representative species from most of the genera in the family. Although percentage sampling was necessarily small, a few examples of species containing these substances were found and some taxonomic suggestions are made and compared with results in the literature. This survey is a basis for further work on the family.     

A molecular phylogenetic investigation of zoothamnium (ciliophora, peritrichia, sessilida)

The gene coding for 18S small subunit ribosomal RNA (ssu rRNA) was sequenced in seven free-living, marine species of the sessiline peritrich genus Zoothamnium. These were Zoothamnium niveum, Zoothamnium alternans, Zoothamnium pelagicum, and four unidentified species. The ssu rRNA gene also was sequenced in Vorticella convallaria, Vorticella microstoma, and in an unidentified, freshwater species of Vorticella. Phylogenetic trees were constructed using these new sequences to test a previously published phylogenetic association between Zoothamnium arbuscula, currently in the family Zoothamniidae, and peritrichs in the family Vorticellidae. Trees constructed by means of neighbor-joining, maximum parsimony, maximum likelihood, and Bayesian inference methods all had similar topologies. The seven new sequences of Zoothamnium species grouped into three well-supported clades, each of which contained a diversity of morphological types. The three clades formed a poorly supported, larger clade that was deeply divergent from Z. arbuscula, which remained more closely associated with vorticellid peritrichs. It is apparent that Zoothamnium is a richly diverse genus and that a much more intensive investigation, involving both morphological and molecular data and a wider selection of species, will be necessary to resolve its phylogeny. A greater amount of molecular diversity than is predicted by morphological data exists within all major clades of sessiline peritrichs that have been included in molecular phylogenies, indicating that characteristics of stalk and peristomial structure traditionally used to differentiate taxa at the generic level and above may not be uniformly reliable.     

Chemicals in aroids: a survey, including new results for polyhydroxy alkaloids and alkylresorcinols

The Araceae is a large, mainly tropical family, many members of which contain bioactive substances which are often either toxic or irritating. Inflorescences frequently emit strong fragrances. The active compounds have not been adequately determined nor is the chemotaxonomy of the family very well known, except for one major study of flavonoids. Two groups of compounds of known bioactivity–alkylresorcinols and nitrogenous sugar analogues–have been sought in representative species from most of the genera in the family. Although percentage sampling was necessarily small, a few examples of species containing these substances were found and some taxonomic suggestions are made and compared with results in the literature. This survey is a basis for further work on the family.     

Barbula cylindrica (Tayl.) Schimp. with rhizoidal tubers

Abstract

Reviews in the 1970s concluded that African moss taxonomy was in a poor state. A comparison is made between the position then and that of today, using examples of recent taxonomic revisions. It is projected that the eventual number of moss taxa in the area may be reduced from over 3000 taxa to around 1300 if a full taxonomic revision is completed. Collecting activity has been greater in recent years, and is continuing. The need for further collecting and a dramatic increase in taxonomic work is emphasised.