Stepping stones towards a new prokaryotic taxonomy

Technological developments provide new insights into prokaryotic evolution and diversity and provoke a continuous need to update taxonomy and revise classification schemes. Our present species concept and definition are being challenged by the growing amount of whole genomic information, which should allow improvements in the natural species definition. The continuous quest for an objective and stable method for sorting strains into coherent homogeneous groups is inherent to prokaryotic systematics and nomenclature. Morphological, biochemical, physiological, phenotypic and chemotaxonomic criteria have been complemented by molecular data and pragmatic, purpose built, species definitions are being replaced by more natural ones based on evolutionary insights. It is imperative to give due consideration to both fundamental and applied aspects of future species concepts and definitions. The present paper discusses the present practice in prokaryotic taxonomy of how this system developed and how it may evolve in the future.     

Structure and function of vertebrate cilia, towards a new taxonomy

In this review, we propose a new classification of vertebrate cilia/flagella and discuss the evolution and prototype of cilia. Cilia/flagella are evolutionarily well-conserved membranous organelles in eukaryotes and serve a variety of functions, including motility and sensation. Vertebrate cilia have been traditionally classified into conventional motile cilia and sensory primary cilia. However, an avalanche of emerging evidence on the variations of cilia has made it almost impossible to classify them in a simple dichotomic manner. For example, conventional motile cilia are also involved in the sensation of bitter taste to facilitate the beating of cilia as a defense system of the respiratory system. On the other hand, the primary cilium, often regarded as a non-motile sensory organelle, has been revealed to be motile in vertebrate embryonic nodes, where they play a crucial role in the determination of left-right asymmetry of the body. Moreover, choroid plexus epithelial cells in the cerebral ventricular system exhibit multiple primary cilia on a single cell. Considering these lines of evidence on the diversity of cilia, we believe the classification of cilia should be based on their structure and function, and include more detailed criteria. Another intriguing issue is how in the evolution of cilia, their function and morphology are combined. For example, has motility been acquired from originally sensory cilia, or vice versa? Alternatively, were they originally hybrid in nature? These questions are inseparable from the classification of cilia per se. We would like to address these conundrums in this review article, principally from the standpoint of differentiation of the animal cell.     

A new taxonomy of the family Teloschistaceae

The lichen family Teloschistaceae is one of the larger families of lichenized fungi. Currently it includes one very large heterogenous genus, Caloplaca, with some 1000 or more species with a vast variation in morphology, anatomy and chemistry. The rest of the family is split into 10–15 smaller genera, each with 20 or fewer species. There is no modern classification of the family based on molecular data. Here we attempt a first phylogenetic evaluation of a large part of the family, including a total of 337 species. Of these, 162 were used in a combined phylogenetic analysis of the ribosomal RNA sequence markers nrITS, nrLSU and mrSSU, using Bayesian inference. We also analysed all species using nrITS data, split into four different analyses. As a result we propose a new classification of the family, where a total of 39 genera are recognized, of which 31 are newly described or resurrected. The new genera are: Athallia, Austroplaca, Bryoplaca, Calogaya, Cerothallia, Flavoplaca, Gondwania, Haloplaca, Orientophila, Pachypeltis, Parvoplaca, Rufoplaca, Shackletonia, Scutaria, Sirenophila, Solitaria, Squamulea, Stellarangia, Teloschistopsis, Usnochroma, Variospora, Villophora and Wetmoreana. Resurrected genera are Blastenia, Dufourea, Follmannia, Gyalolechia, Leproplaca, Polycauliona, Pyrenodesmia and Xanthocarpia. The species Orientophila subscopularis is described as new. A third subfamily, Teloschistoideae, is proposed to accommodate the genus Teloschistes and related genera, parallel to the two previously recognized subfamilies Xanthorioideae and Caloplacoideae. We also show the large plasticity in both morphological and anatomical characters between closely related species within genera, indicating the low value of these as evolutionary markers. The secondary chemistry is a better marker in some parts of the family. We recognize a large number of geographically delimited clades with clear centres of evolution, but often showing large variation in morphology and anatomy.     

Phylogeny, biogeography and a new taxonomy for the Gecarcinucoidea Rathbun, 1904 (Decapoda: Brachyura)

Phylogenetic relationships of gecarcinucoid freshwater crabs were investigated, based on morphology of the male second gonopod. In addition, a comparison of sequences from the mitochondrial large subunit rRNA gene helped to resolve the phylogeny of this group and relationships to other Old World freshwater crabs. As a result, we recognise two sister groups within the Gecarcinucoidea, the African Deckeniidae and the Asian Gecarcinucidae. Deckeniidae includes three monophyletic clades, the Deckeniinae in East Africa and on the Seychelles, the West African Globonautinae and the Malagasy Hydrothelphusinae. Gecarcinucidae comprises two sister groups, the Gecarcinucinae with representatives in Sri Lanka, India and southeast Asia, and the Parathelphusinae in India, southeast Asia, the Sundaic Islands and Australia. Interpretation of our phylogenetic results leads us to propose a new biogeographic hypothesis for the Gecarcinucoidea. Most likely, the gecarcinucoid freshwater crabs have an African origin; their distribution can be explained by successive events of dispersal. This model can be correlated with palaeogeographical and palaeoclimatological data for the Cenozoic, suggesting a gecarcinucoid dispersal to Asia via the “Lemurian Stepping-Stones”, a chain of islands in the West-Indian Ocean that were emergent in times of low sea levels during the Oligocene.     

CHROMOSOMAL LOCALIZATION OF REPETITIVE DNA IN THE NEWT, TRITURUS

The repetitive DNA sequences of the newt, Triturus viridescens, have been studied by nucleic acid hybridization procedures. Complementary RNA was synthesized enzymatically from unfractionated newt DNA. This RNA hybridized strongly to the centromeric regions of both somatic and lampbrush chromosomes It also bound to other loci scattered along the lengths of the chromosomes The amplified ribosomal DNA in the multiple oocyte nucleoli was demonstrated by in situ hybridization     

Integrative taxonomy reveals a new species of Callisto (Lepidoptera,Gracillariidae) in the Alps

Europe has one of the best-known Lepidopteran faunas in the world, yet many species are still being discovered, especially in groups of small moths. Here we describe a new gracillariid species from the south-eastern Alps, Callisto basistrigella Huemer, Deutsch & Triberti, sp. n. It shows differences from its sister species Callisto coffeella in morphology, the barcode region of the cytochrome c oxidase I gene and the nuclear gene histone H3. Both Callisto basistrigella and Callisto coffeella can co-occur in sympatry without evidence of admixture. Two Callisto basistrigella specimens show evidence of introgression. We highlight the importance of an integrative approach to delimit species, combining morphological and ecological data with mitochondrial and nuclear sequence data. Furthermore, in connection with this study, Ornix blandella Müller-Rutz, 1920, syn. n. is synonymized with Callisto coffeella (Zetterstedt, 1839).     

Notes on the taxonomy of Stentor Oken (Protozoa, Ciliophora) and a description of a new species

The taxonomy of a heterotrichous ciliate genus Stentor has beeninvestigated on the basis of the author's old notebooks andphotographs of the species found in and around Hiroshima City,Japan. In addition to the ten known species that were found,including the ones synonymized by Foissner and Wölfl (Foissnerand Wölfl, 1994), a new species was also present and isdescribed in this article. The results of grafting an organismof one species with another from either the same or a differentspecies are also given. Use of stock-cultured, live specimensis recommended to observe the characters overlooked or disregardedby Foissner and Wölfl (Foissner and Wölfl, 1994) andto perform the grafting experiment which gives subsidiary informationon the taxonomic status of the strains concerned.     

'NUAGE'-CHROMOSOME ASSOCIATION IN METAPHASE SPERMATOGONIA OF THE NEWT, CYNOPUS PYRRHOGASTER

The 'nuage', an electron dense cytoplasmic component specific to the germ line cell, was found to be closely associated with a metaphase chromosome in the spermatogenic cell of the newt, Triturus (Cynops) pyrrhogaster. This finding suggests a possible relationship between both components at a certain stage of spermatogenesis.     

生物分类学的新动向--DNA条形编码

过去的一年中 ,DNA条形编码 (DNABarcoding)成为生物分类学中引人注目的新方向。DNA条形编码 ,根据对一个统一的目标基因DNA序列的分析 ,达到物种鉴定的目的 ,它操作的简便性和高效性将以我们无法想象的速度加快物种鉴定和进化历史研究的步伐 ,但国际上对此的争论也不少。本文综述了DNA条形编码的原理、操作过程及最新进展 ,讨论了其可能存在的问题     

Toward a molecular taxonomy

Summary The concepts of a super information source and ensemble averaging are used to estimate the amount of information stored in protein andt-RNA sequences. Specifically applied to cytochrome c and hemoglobins, information measures analogous to those found to be highly significant for DNA pair frequency data (D₂ vs.R) by Gatlin (1968) prove to be extremely highly correlated with organism complexity. Super source stability and the possible taxonomic utility of the extraordinary clusterings obtained are discussed. A restriction on the construction of ancestral sequences and a possible handle on homology are also detailed.     

Pythium carbonicum,a new species isolated from a spoil heap in northern France,the ITS region,taxonomy and comparison with related species

Pythium carbonicum (F-72) sp. nov. was found in soil samples taken on the top of a spoil heap in northern France. The morphology of this new species resembles that of a recently described species: Pythium megacarpum. However, the antheridial and oogonial characteristics of this new species are unique, and the comparison of its ITS region of the nuclear ribosomal DNA indicates that this species is also related to the genus Phytophthora. The fungus does not sporulate, the sporangia germinate directly into mycelium through germ tubes. The oogonia of P. carbonicum are smooth-walled and also papillated, and are provided with monoclinous and diclinous antheridia that wrap around, forming a complicated knot. Morphological features of this new species, together with the sequences of the ITS region of its nuclear ribosomal DNA and its comparison with related species are discussed here.     

Antispila oinophylla new species (Lepidoptera, Heliozelidae), a new North American grapevine leafminer invading Italian vineyards: taxonomy, DNA barcodes and life cycle

A grapevine leafminer Antispila oinophylla van Nieukerken & Wagner, sp. n., is described both from eastern North America (type locality: Georgia) and as a new important invader in North Italian vineyards (Trentino and Veneto Region) since 2006. The species is closely related to, and previously confused with Antispila ampelopsifoliella Chambers, 1874, a species feeding on Virginia creeper Parthenocissus quinquefolia (L.) Planchon., and both are placed in an informal Antispila ampelopsifoliella group. Wing pattern, genitalia, and DNA barcode data all confirm the conspecificity of native North American populations and Italian populations. COI barcodes differ by only 0-1.23%, indicating that the Italian populations are recently established from eastern North America. The new species feeds on various wild Vitis species in North America, on cultivated Vitis vinifera L. in Italy, and also on Parthenocissus quinquefolia in Italy. North American Antispila feeding on Parthenocissus include at least two other species, one of which is Antispila ampelopsifoliella. Morphology and biology of the new species are contrasted with those of North American Antispila Hübner, 1825 species and European Holocacista rivillei (Stainton, 1855). The source population of the introduction is unknown, but cases with larvae or pupae, attached to imported plants, are a likely possibility. DNA barcodes of the three European grapevine leafminers and those of all examined Heliozelidae are highly diagnostic. North American Vitaceae-feeding Antispila form two species complexes and include several as yet unnamed taxa. The identity of three out of the four previously described North American Vitaceae-feeding species cannot be unequivocally determined without further revision, but these are held to be different from Antispila oinophylla. In Italy the biology of Antispila oinophylla was studied in a vineyard in the Trento Province (Trentino-Alto Adige Region) in 2008 and 2009. Mature larvae overwinter inside their cases, fixed to vine trunks or training stakes. The first generation flies in June. An additional generation occurs from mid-August onwards. The impact of the pest in this vineyard was significant with more than 90% of leaves infested in mid-summer. Since the initial discovery in 2006, the pest spread to several additional Italian provinces, in 2010 the incidence of infestation was locally high in commercial vineyards. Preliminary phylogenetic analyses suggest that Antispila is paraphyletic, and that the Antispila ampelopsifoliella group is related to Coptodisca Walsingham, 1895, Holocacista Walsingham & Durrant, 1909 and Antispilina Hering, 1941, all of which possess reduced wing venation. Vitaceae may be the ancestral hostplant family for modern Heliozelidae.     

CHANGES IN NUCLEOLI AT MATURATION OF NEWT OOCYTE

Changes in the nucleoli of maturing oocytes and the eggs of Cynops pyrrhogaster were studied with light and electron microscopy. Extrachromosomal nucleoli moved toward the center of the germinal vesicle in response to the maturation stimulus, released presumed ribosomal ribonucleoprotein, and further moved toward the center of the nucleus to form an aggregate with chromosomes which behaved in a similar manner. A few. ball-shaped nucleolar masses were formed from this aggregate, leaving the chromosomes and probably the extrachromosomal nucleolar organizer. The chromosomes then proceeded to the first meiotic metaphase. The nucleolar masses were surrounded by a layer of mitochondria and became smaller with formation of pinched-off fragments, which were also surrounded by mitochondria, during the time the egg was moving down the oviduct. Only fragments were observed in the subcortical area of the animal hemisphere of the egg after reaching the lowest part of the oviduct.     

REACTION TO VISUAL FLICKER IN THE NEWT TRITURUS

The flicker response curve for the newt Triturus viridescens (water phase) has much the same quantitative structure as that found with various fresh-water teleosts at the same temperature (21.5°). The variability of critical intensity and of critical flash frequency likewise follows the same rules. The cone portion of the F - log I curve is much more widely spread, however. This, and the rather low maximum to which the rod curve rises, produce a considerable overlapping of the two parts additively fused. In addition, and to an extent which differs in various individuals, there is apparent a slight departure from the probability integral form of the cone curve. Reasons are given for considering that this is possibly connected with the role of an additional (small) number of (perhaps temporary, or developmental) retinal elements in addition to the typical rods and cones.     

A UNIQUE JUNCTIONAL STRUCTURE FOUND IN BLASTULA CELLS OF THE NEWT, TRITURUS PYRRHOGASTER

The outermost cell layer of the animal half of the newt blastula ( Triturus pyrrhogaster ) was examined to investigate intercellular junctions by transmission and scanning electron microscopy. A unique structure is observed at the terminal region of the intercellular junction. The structures are cytoplasmic ridges elevated from the cell surfaces, and their inner part is filled with spaces of various sizes. It is supposed that these ridges result from the encounter of cytoplasmic folds protruding from two neighboring cells.
Below the ridges, there is a short close junctional area which is followed by a long region of intercellular space intermittently bridged by cytoplasmic projections. Microvillus-like cytoplasmic processes on the apical cell surfaces, and microfilaments and microtubules in subsurface regions are observed in this material as in many other embryonic cells of amphibians.