Research note: Amorphochlora amoebiformis gen. et comb. nov. (Chlorarachniophyceae)

A chlorarachniophycean alga, Lotharella amoebiformis, which has been classified in the genus Lotharella is placed into a new genus Amorphochlora gen. nov., based on its phylogenetic position, which has been clarified by the recently accumulated molecular phylogenetic information, and the morphological difference between the vegetative cells of the Lotharella species. Following this taxonomic treatment, a new combination Amorphochlora amoebiformis comb. nov., is proposed.     

Detection of Seven Major Evolutionary Lineages in Cyanobacteria Based on the 16S rRNA Gene Sequence Analysis with New Sequences of Five Marine Synechococcus Strains

Although molecular phylogenetic studies of cyanobacteria on the basis of the 16S rRNA gene sequence have been reported, the topologies were unstable, especially in the inner branchings. Our analysis of 16S rRNA gene phylogeny by the maximum-likelihood and neighbor-joining methods combined with rate homogeneous and heterogeneous models revealed seven major evolutionary lineages of the cyanobacteria, including prochlorophycean organisms. These seven lineages are always stable on any combination of these methods and models, fundamentally corresponding to phylogenetic relationships based on other genes, e.g., psbA, rbcL, rnpB, rpoC, and tufA. Moreover, although known genotypic and phenotypic characters sometimes appear paralleled in independent lineages, many characters are not contradictory within each group. Therefore we propose seven evolutionary groups as a working hypothesis for successive taxonomic reconstruction. New 16S rRNA sequences of five unicellular cyanobacterial strains, PCC 7001, PCC 7003, PCC 73109, PCC 7117, and PCC 7335 of Synechococcus sp., were determined in this study. Although all these strains have been assigned to ``marine clusters B and C,' they were separated into three lineages. This suggests that the organisms classified in the genus Synechococcus evolved diversely and should be reclassified in several independent taxonomic units. Moreover, Synechococcus strains and filamentous cyanobacteria make a monophyletic group supported by a comparatively high statistical confidence value (80 to 100%) in each of the two independent lineages; therefore, these monophylies probably reflect the convergent evolution of a multicellular organization. Received: 3 September 1998 / Accepted: 30 November 1998     

Synechococcus: 3 billion years of global dominance

Cyanobacteria are among the most important primary producers on the Earth. However, the evolutionary forces driving cyanobacterial species diversity remain largely enigmatic due to both their distinction from macro‐organisms and an undersampling of sequenced genomes. Thus, we present a new genome of a Synechococcus‐like cyanobacterium from a novel evolutionary lineage. Further, we analyse all existing 16S rRNA sequences and genomes of Synechococcus‐like cyanobacteria. Chronograms showed extremely polyphyletic relationships in Synechococcus, which has not been observed in any other cyanobacteria. Moreover, most Synechococcus lineages bifurcated after the Great Oxidation Event, including the most abundant marine picoplankton lineage. Quantification of horizontal gene transfer among 70 cyanobacterial genomes revealed significant differences among studied genomes. Horizontal gene transfer levels were not correlated with ecology, genome size or phenotype, but were correlated with the age of divergence. All findings were synthetized into a novel model of cyanobacterial evolution, characterized by serial convergence of the features, that is multicellularity and ecology.     

Analysis and identification of ADP-ribosylated proteins of <Emphasis Type="Italic">Streptomyces coelicolor</Emphasis> M145

Mono-ADP-ribosylation is the enzymatic transfer of ADP-ribose from NAD⁺ to acceptor proteins catalyzed by ADP-ribosyltransferases. Using m-aminophenylboronate affinity chromatography, 2D-gel electrophoresis, in-gel digestion and MALDI-TOF analysis we have identified eight in vitro ADP-ribosylated proteins in Streptomyces coelicolor, which can be classified into three categories: (i) secreted proteins; (ii) metabolic enzymes using NAD⁺/NADH or NADP⁺/NADPH as coenzymes; and (iii) other proteins. The secreted proteins could be classified into two functional categories: SCO2008 and SC05477 encode members of the family of periplasmic extracellular solute-binding proteins, and SCO6108 and SC01968 are secreted hydrolases. Dehydrogenases are encoded by SC04824 and SC04771. The other targets are GlnA (glutamine synthetase I., SC02198) and SpaA (starvation-sensing protein encoded by SC07629). SCO2008 protein and GlnA had been identified as ADP-ribosylated proteins in previous studies. With these results we provided experimental support for a previous suggestion that ADP-ribosylation may regulate membrane transport and localization of periplasmic proteins. Since ADP-ribosylation results in inactivation of the target protein, ADP-ribosylation of dehydrogenases might modulate crucial primary metabolic pathways in Streptomyces. Several of the proteins identified here could provide a strong connection between protein ADP-ribosylation and the regulation of morphological differentiation in S. coelicolor.     

Molecular phylogeny of Geoplaninae (Platyhelminthes) challenges current classification: proposal of taxonomic actions

Despite likely being the most diverse group within the Tricladida, the systematics of land planarians (Geoplanidae) has received minor attention. The most species‐rich ingroup, the subfamily Geoplaninae, is restricted to the Neotropics. The systematics of Geoplaninae remains uncertain. Unique features supporting the genera are scanty; moreover, parts of the known species have been poorly described, making comparative studies difficult. Likewise the evolutionary relationships among land planarians remain insufficiently understood. In the present study, a phylogenetic hypothesis for selected taxa of Geoplaninae based on the molecular data is presented and discussed in the light of morphological features. Our phylogenetic inference is based on the fragments of three nuclear regions (18S, 28S rDNA and EF‐1α) and a mitochondrial marker (cytochrome oxidase I) for which we considered three optimality criteria (parsimony, maximum likelihood and Bayesian inference). Although our data provide little support for most basal nodes, our phylogenetic trees show a number of well‐supported clades, unveiling morphologically homogeneous groups. According to these results, we propose to separate Geoplana into Barreirana (formerly considered a subgenus), Cratera gen. n., Imbira gen. n., Matuxia gen. n., Obama gen. n. and Paraba gen. n., emend the diagnoses of Barreirana, Geoplana, Notogynaphallia, Pasipha and Xerapoa and review the classification of the species within these genera. For Geoplana goetschi sensu Marcus, (1951), a new name is proposed.     

The influence of spatial scale on the congruence of classifications circumscribing morphological units of biodiversity

Aim The ‘taxonomic impediment’ has led to a growing trend in ecology and conservation biology to use operational surrogates for species within the context of a particular research project. Because such ‘parataxonomic’ classifications are typically spatially limited in scope, we examined the influence of increasing spatial scale on the congruence of two such approaches with a more traditional taxonomic classification. Location Sturt National Park, north‐western New South Wales, Australia. Methods Specimens of two ant genera, Camponotus and Rhytidoponera, were classified by three independent methods. The ‘parataxonomic’ classification assigned specimens to morphospecies without specialist taxonomic expertise; the ‘taxonomic’ classification assigned specimens to either described species or, where this was not possible, to operational taxonomic units (OTUs) using specialist taxonomic expertise; the ‘phenetic’ classification assigned specimens to putative species using a K‐means partitioning algorithm on basic morphometric data. Specimens of each genus were pooled into ‘assemblages’, which were defined at multiple spatial scales using a nested sampling design. Congruence in the interspecimen relationships of the different classifications was tested for each assemblage using pair‐wise Mantel correlations. Results Classification congruence tended to decrease with increasing spatial scale. There were, however, clear differences between the genera. Parataxonomic–taxonomic congruence was consistently greater for Camponotus, while phenetic–taxonomic congruence showed the opposite pattern. Conclusions Observed patterns in classification congruence are attributed to two principal causes: (i) within‐species morphological variation, including ecotypic variation in Rhytidoponera and caste polymorphism in Camponotus; and (ii) a limit to the morphological similarity of potentially competing species at small spatial scales. Regardless of cause, the decline in agreement as the spatial scale of observation is increased has important implications for the measurement of biodiversity, particularly when comparing samples over regional, continental, and global scales.     

Classification of Reynolds phytoplankton functional groups using individual traits and machine learning techniques

相似文献   

ACARYOCHLORIS MARINA GEN. ET SP. NOV. (CYANOBACTERIA), AN OXYGENIC PHOTOSYNTHETIC PROKARYOTE CONTAINING CHL D AS A MAJOR PIGMENT1

The phylogenetic position of an oxygenic photosynthetic prokaryote containing chl d as a major pigment, which have been tentatively named “Acaryochloris marina,” was analyzed using small subunit rDNA sequences. Phylogenetic relationships inferred among A. marina, selected strains from the Cyanobacteria, and plastids showed that A. marina was within the cyanobacterial radiation. The A. marina lineage diverged independently from other phylogenetic subgroups of the Cyanobacteria. No organism was found to be identical or related closely to A. marina by a similarity search and phylogenetic analysis. Based on these results, in addition to the reported characteristics of the cell morphology, pigment composition, and photosynthesis, a new taxon, Acaryochloris marina Miyashita et Chihara gen. et sp. nov., is formally proposed for the oxy‐genic photosynthetic prokaryote.     

A NEW LOOK AT AN ANCIENT ORDER: GENERIC REVISION OF THE BANGIALES (RHODOPHYTA)1

The red algal order Bangiales has been revised as a result of detailed regional studies and the development of expert local knowledge of Bangiales floras, followed by collaborative global analyses based on wide taxon sampling and molecular analyses. Combined analyses of the nuclear SSU rRNA gene and the plastid RUBISCO LSU (rbcL) gene for 157 Bangiales taxa have been conducted. Fifteen genera of Bangiales, seven filamentous and eight foliose, are recognized. This classification includes five newly described and two resurrected genera. This revision constitutes a major change in understanding relationships and evolution in this order. The genus Porphyra is now restricted to five described species and a number of undescribed species. Other foliose taxa previously placed in Porphyra are now recognized to belong to the genera Boreophyllum gen. nov., Clymene gen. nov., Fuscifolium gen. nov., Lysithea gen. nov., Miuraea gen. nov., Pyropia, and Wildemania. Four of the seven filamentous genera recognized in our analyses already have generic names (Bangia, Dione, Minerva, and Pseudobangia), and are all currently monotypic. The unnamed filamentous genera are clearly composed of multiple species, and few of these species have names. Further research is required: the genus to which the marine taxon Bangia fuscopurpurea belongs is not known, and there are also a large number of species previously described as Porphyra for which nuclear SSU ribosomal RNA (nrSSU) or rbcL sequence data should be obtained so that they can be assigned to the appropriate genus.     

Bacterial composition of sponges,sediment and seawater in enclosed and open marine lakes in Ha Long Bay Vietnam

ABSTRACT

Marine lakes are landlocked bodies of seawater, isolated to varying degrees from the surrounding marine habitat. Isolated lakes generally have lower pH values, salinities and higher temperatures than more open lakes. We used a 16S rRNA gene barcoded pyrosequencing approach to study the bacterial communities of two sponge species, sediment and seawater in one enclosed and two open marine lakes. Bacterial communities of the sponge Spheciospongia solida mainly consisted of Proteobacteria, Cyanobacteria and Bacteroidetes. In contrast, Proteobacteria, Chloroflexi and Acidobacteria dominated the bacterial communities of the sponge Spongia ceylonensis. Although only a limited amount of samples were collected, both water and S. ceylonensis sponge had higher relative abundances of Cyanobacteria in the enclosed lake, which mainly consisted of OTUs assigned to the genus Synechococcus. This is in line with a number of previous studies, which have shown that environmental conditions found within low pH environments such as marine lakes benefit the growth of Synechococcus spp. Future studies should address the mechanism by which Synechococcus spp. may help host sponges and their bacterial communities adapt to low pH conditions in isolated marine lakes and other low-pH environments.     

Phytoplankton community structure of a deep subalpine Italian Lake (Lake Orta,N. Italy) four years after the recovery from acidification by liming

The phytoplankton succession in Lake Orta, heavy metals and ammonium polluted for decades and subjected to liming intervention in 1989–90, was studied during 1994. The existence of three main succession stages, with different structures of the community emerged. Chlorophyta are the most important taxonomic group in every season. The spring community was dominated by chlorophytes, Dinobryon sertularia and Kephyrion sp., the summer by Synedra sp. and Westella botryoides, the autumn by Rhizosolenia eriensis and W. botryoides, the winter by Synedra sp., R. eriensis and Synechococcus sp. The abundance of Chlorophyta, less important in other deep subalpine lakes, and the dominance of taxa able to thrive in polluted environments, could be related to the presence of trace metals in the sediments.     

A new scolenaspidid (Osteostraci, Vertebrata) from the Lower Devonian of Podolia, Ukraine

Anew osteostracan genus and species,Victoraspis longicornualis n. gen., n. sp., is described based on material from Rakovets’, present day Ukraine. This new taxon shares characters with the two generaStensiopelta Denison, 1951 andZychaspis Janvier, 1985. A phylogenetic analysis supports the position ofVictoraspis as the sister group to a monophyleticStensiopelta, while the interrelationships of the various species ofZychaspis are poorly resolved. A morphometric analysis is carried out in an attempt to further resolve the taxonomic affinity. This analysis groups all examinedZychaspis species closely together, and further supports the establishment ofVictoraspis as separate genus.      

Quantitative parameters of synaptic apparatus in the ventral nucleus of the medial geniculate body of the cat

The synaptic apparatus in the ventral nucleus of the medial geniculate body (MGBv) of the cat was examined using electron microscopy and stereological methods, which made it possible to measure the synaptic density. Within 7015 µm² of examined sections, 1586 presynaptic terminal (PST) profiles were found, which corresponds to 226.0·10³ PST per 1 mm² of section surface. The PSP were classified into five groups:RL,RS,F,P, andUT, in accordance with their ultrastructural pattern (dimension of PST profile, dimension and shape of synaptic vesicles, and type of synaptic contact, SC) [18–22]. On the above surface, there were 1012 SC formed by PST of different groups, which corresponds to 144.0·10³ SC per 1 mm² of section surface. TheRL-,RS-,F-,P-, andUT-type PST formed 14.8%, 50.1%, 13.1%, 16.8%, and 5.2% of analyzed SC, respectively. The calculated mean SC numerical density equalled (260.8±54.8)·10⁶ SC per 1 mm³ of fixed MGBv tissue. Among them, 40.2·10⁶ (15.4%) belonged toRL-PST, i.e., to axonal terminals of thecolliculus inferior neurons; 130.2·10⁶ (49.9%) toRS-PST, i.e., mostly to axonal terminals of the auditory cortex neurons; and 33.9·10⁶ (13.0%) toF-PST, i.e., to axons of the GABA-ergic interneurons and neurons of the perigeniculate division of the reticular thalamic nucleus. Group-P PST, i.e., terminal structures of the dendritic arborizations of interneurons, formed 42.7·10⁶ (16.4%) SC per 1 mm³, and 13.8·10⁶ (5.3%) SC belonged toUT-PST, i.e., to terminals of unidentified nature. Among 260.8·10⁶ SC in 1 mm³ of tissue, only 23.8·10⁶ (9% of total number)RL-SC, localized on the relay neurons, are directly involved in the MGBv relay function. All other SC transmit control influences from various structures of the nervous system, and provide adjustment of relay function to the constantly changing environmental conditions and varying status of an orgamism. The mean number of SC, localized on an averaged MGBv relay neuron, was calculated as 9100. Among them, about 1200 SC belong toRL-PST, 5200 SC toRS-PST, 1200 SC toF-PST, 1100 SC toP-PST, and 400 SC toUT-PST.Neirofiziologiya/Neurophysiology, Vol. 27, No. 3, pp. 208–219, May–June, 1995.     

Phylogeny and genus-level classification of mantellid frogs (Amphibia, Anura)

We propose a novel classification of frogs in the family Mantellidae, based on published phylogenetic information and on a new analysis of molecular data. Our molecular tree for 53 mantellid species is based on 2419 base pairs of the mitochondrial 12S rRNA, 16S rRNA, tRNAVal and cytochrome b genes, and of the nuclear rhodopsin gene. Because the genus Mantidactylus Boulenger sensu lato is confirmed to be paraphyletic with respect to Mantella Boulenger, and is highly diverse in morphology and reproductive biology, we propose to partition Mantidactylus into seven genera by elevating four subgenera to genus rank (Blommersia Dubois, Guibemantis Dubois, Spinomantis Dubois, and Gephyromantis Methuen) and creating two new genera (Boehmantis gen. n. and Wakea gen. n.). In addition, we create the new subgenera Boophis (Sahona) subgen. n., Gephyromantis (Duboimantis) subgen. n., G. (Vatomantis) subgen. n., and Mantidactylus (Maitsomantis) subgen. n. The following species are transferred to Spinomantis, based on their phylogenetic relationships: S. elegans (Guibé) comb. n. (formerly in Mantidactylus subgenus Guibemantis); S. bertini (Guibé) comb. n. and S. guibei (Blommers-Schlösser) comb. n. (both formerly in Mantidactylus subgenus Blommersia); S. microtis (Guibé) comb. n. (formerly in Boophis Tschudi). Within Boophis, the new B. mandraka species group and B. albipunctatus species group are established. Boophis rhodoscelis (Boulenger) is transferred to the B. microtympanum group. The following five species are revalidated: Mantidactylus bellyi Mocquard and M. bourgati Guibé (not junior synonyms of M. curtus (Boulenger)); M. cowanii (Boulenger) (not syn. M. lugubris (Duméril)); M. delormei Angel (not syn. M. brevipalmatus Ahl); Mantella ebenaui (Boettger) (not syn. M. betsileo (Grandidier)). The new classification accounts for recent progress in the understanding of the phylogeny and natural history of these frogs, but it is still tentative for a number of species. Future modifications may be necessary, especially as concerns species now included in Gephyromantis and Spinomantis.Full article published online at: http://www.senckenberg.de/odes/06-11.htm     

Total evidence phylogenetic analysis and reclassification of Euschistus Dallas within Carpocorini (Hemiptera: Pentatomidae: Pentatominae)

Robust phylogenetic hypotheses have become key for studies addressing the evolutionary biology and ecology of various groups of organisms. In the species‐rich heteropteran superfamily Pentatomoidea, phylogenies at lower taxonomic levels are still scarce and mostly employ exclusively morphological data. In this study, we conducted a total evidence phylogeny focusing on the tribe Carpocorini (Pentatomidae), using morphological data and four DNA markers (COI, Cytb, 16S and 28S rDNA; ～2330 bp; 32 taxa) in order to investigate the relationships within Euschistus Dallas, one of the most speciose pentatomid genera, and between Euschistus and related genera. Our hypotheses generated by maximum likelihood and Bayesian inference show that the current taxonomic composition and classification of Euschistus and allied genera are in need of revision. Euschistus was recovered as nonmonophyletic, with the subgenera forming four independent lineages: Euschistus (Euschistus) and Euschistus (Lycipta) Stål are sister groups; Euschistus (Euschistomorphus) Jensen‐Haarup is more closely related to Dichelops Spinola and Agroecus Dallas; and Mitripus Rolston is divided into two clades closely related to Sibaria Stål and Ladeaschistus Rolston. We chose not to change the classification of E. (Euschistomorphus) until further data become available, and propose to split Euschistus into three genera with the exclusion of Euschistus (Mitripus) and all of its species. Here we elevate Mitripus to genus rank to include M. acutus comb.n. , M. convergens comb.n. and M. legionarius comb.n. , and propose Adustonotus Bianchi gen.n. to include A. anticus comb.n. , A. latus comb.n. , A. tauricornis comb.n. , A. grandis comb.n. , A. hansi comb.n. , A. paranticus comb.n. , A. irroratus comb.n. and A. saramagoi comb.n. We also provide identification keys to the genera Adustonotus gen.n. , Ladeaschistus, Mitripus n. rank and Sibaria, here defined as the Mitripus genus group, and to the species of Mitripus and Adustonotus gen.n. Our results provide insights into the current status of the classification of the Pentatomidae, suggesting the need for phylogenetic analyses at different taxonomic levels within stink bugs. This published work has been registered in ZooBank, http://zoobank.org/urn:lsid:zoobank.org:pub:E09D2675‐0F2B‐4AAE‐9837‐257E0B18BC52 .     

Inhibition of dinoflagellate growth by extracts of barley straw (Hordeum vulgare)

Growth of dinoflagellates representing three orders, the Gymnodiniales,Peridiniales, and the Prorocentrales was examined following treatment withbarley straw extract. Selected dinoflagellate taxa showed growth responsessimilar to those reported for freshwater algae including: inhibition(Gyrodinium galatheanum, Gymnodiniumsanguineum, Heterocapsa triquetra andH. pygmaea); stimulation (Gyrodinium instriatum,Prorocentrum minimum and P. micans); and no effect(Gyrodinium estuariale, G. uncatenum,Ceratium furca, Peridinium sp.).Although barley straw extracts do not appear to have value as a universalmanagement tool for dinoflagellates, they may have potential in management ofspecific taxa and possibly taxonomic groups.