Phylogenetic Relationships of Orders Within the Class Colpodea (Phylum Ciliophora) Inferred from Small Subunit rRNA Gene Sequences

Molecular analyses have been used recently to refine our knowledge of phylogenetic relationships within the ciliated protozoa (phylum Ciliophora). A current Hennigian phylogeny of the orders in the class Colpodea, based on light and electron microscopic analyses, makes three important assumptions with regard to apomorphic character states, namely, (1) that the kreyellid silver line evolved early in colpodean phylogeny, separating bryometopids, such as Bryometopus, from all other colpodeans; (2) that the macro–micronuclear complex is an autapomorphy of the cyrtolophosidids, such as Platyophrya; and (3) that merotelokinetal stomatogenesis is an apomorphic character of colpodids, such as Colpoda, Bresslaua, and Pseudoplatyophrya. These predictions of relationships within the class Colpodea were investigated by determining the complete small subunit rRNA gene sequences for the colpodid Bresslaua vorax, the grossglockneriid Pseudoplatyophrya nana, and the cyrtolophosidid Platyophrya vorax and a partial sequence for the bryometopid Bryometopus sphagni. These sequences were combined with the previously published complete SSrRNA sequences for the colpodid Colpoda inflata and the bursariomorphid Bursaria truncatella. The affiliations were assessed using both distance matrix and maximum-parsimony analyses. The tree topologies for the class Colpodea were identical in all analyses, with bootstrap support for bifurcations always exceeding 60%. The results suggest the following. (1) Since the clade including Bryometopus and its sister taxon, Bursaria, is never basal, the kreyellid silver-line system evolved later in colpodean phylogeny and does not separate bryometopids from all other colpodeans. (2) Since Platyophrya is always the sister taxon to the other five genera, there is a fundamental phylogenetic significance for its macro–micronuclear complex. (3) Since the colpodids, Colpoda, Bresslaua, and Pseudoplatyophrya, always group in one clade, merotelokinetal stomatogenesis appears to be a derived character state. Received: 30 June 1998 / Accepted: 3 December 1998     

Phylogeny of Six Genera of the Subclass Haptoria (Ciliophora,Litostomatea) Inferred from Sequences of the Gene Coding for Small Subunit Ribosomal RNA

ABSTRACT. The small subunit ribosomal RNA genes of nine species belonging to six genera of litostome ciliates, namely Amphileptus aeschtae, Chaenea teres, Chaenea vorax, Lacrymaria marina, Litonotus paracygnus, Loxophyllum sp.‐GD‐070419, Loxophyllum jini, Loxophyllum rostratum, and Phialina salinarum, were sequenced for the first time. Phylogenetic trees were constructed using different methods to assess the inter‐ and intra‐generic relationships of haptorians, of which Chaenea, Lacrymaria, Litonotus, and Phialina were analyzed for the first time based on molecular data. Monophyly of the order Pleurostomatida was strongly confirmed, and the two existing families of pleurostomatids, created on the basis of morphology, were confirmed by molecular evidence. Within the Pleurostomatida, Siroloxophyllum utriculariae occupied a well‐supported position basal to the Loxophyllum clade, supporting the separation of these genera from one another. Both the subclass Haptoria and the order Haptorida were partially unresolved, possibly paraphyletic assemblages of taxa in all analyses, creating doubts about the traditional placement of some haptorid taxa. The existing sequence of L. rostratum in GenBank (DQ411864) was conspicuously different from that of the isolate from Qingdao, China sequenced in the present work, indicating that they are different species. The isolate from Qingdao was verified as L. rostratum by morphological analysis, and the published morphology of existing GenBank record of L. rostratum is different from it. Based on both morphological and molecular evidence, the latter may be congeneric with an undescribed species of Loxophyllum from Guangdong Province, China.     

Secondary Structure and Molecular Evolution of the Mitochondrial Small Subunit Ribosomal RNA in Agaricales (Euagarics clade,Homobasidiomycota)

The complete sequences and secondary structures of the mitochondrial small subunit (SSU) ribosomal RNAs of both mostly cultivated mushrooms Agaricus bisporus (1930 nt) and Lentinula edodes (2164 nt) were achieved. These secondary structures and that of Schizophyllum commune (1872 nt) were compared to that previously established for Agrocybe aegerita. The four structures are near the model established for Archae, Bacteria, plastids, and mitochondria; particularly the helices 23 and 37, described as specific to bacteria, are present. Within the four Agaricales (Homobasidiomycota), the SSU-rRNA core is conserved in size (966 to 1009 nt) with the exception of an unusual extension of 40 nt in the H17 helix of S. commune. The four core sequences possess 76% of conserved positions and a cluster of C in their 3 end, which could constitute a signal involved in the RNA maturation process. Among the nine putative variable domains, three (V3, V5, V7) do not show significant length variations and possess similar percentages of conserved positions (69%) than the core. The other six variable domains show important length variations, due to independent large size inserted/deleted sequences, and higher rates of nucleotide substitutions than the core (only 31% of conserved positions between the four species). Interestingly, the inserted/deleted sequences are located in few preferential sites (hot spots for insertion/deletion) where they seem to arise or disappear haphazardly during evolution. These sites are located on the surface of the tertiary structure of the 30S ribosomal subunit, at the beginning of hairpin loops; the insertions lead to a lengthening of existing hairpins or to branching loops bearing up to five additional helices.     

The systematics of Seminavis (Bacillariophyta) : the lost identities of Amphora angusta,A. ventricosa and A. macilenta

Amphora angusta Gregory, Amphora ventricosa Gregory and Amphora macilenta Gregory have been misunderstood for the last 140 years. Gregory described these species from sublittoral sediments off the west coast of Scotland. Although the illustrations were excellent for their time (1857), it is impossible to be confident of identification using Gregory's paper, and subsequent authors have created such confusion that records of these taxa must be regarded as untrustworthy unless backed by photographic evidence. In this paper, the first to describe in detail the recently established genus Seminavis, we show that A. angusta is in fact a species of Amphora Ehrenberg, whereas A. ventricosa sensu Gregory represents two independent species of the genus Seminavis D. G. Mann, namely Seminavis ventricosa (Gregory) Garcia-Baptista (non S. ventricosa sensu Garcia-Baptista 1993) and Seminavis arranensis Danielidis & D. G. Mann, sp. nov. The form usually known as A. ventricosa is neither of these and requires a new name, Seminavis robusta Danielidis & D. G. Mann, sp. nov. The long forgotten and misclassified species A. macilenta Gregory is shown to be yet another Seminavis species, requiring a new combination as S. macilenta (Gregory) Danielidis & D. G. Mann, comb. nov.; contrary to previous claims, it is separate from A. ergadensis Gregory, which is a true Amphora. Valve and girdle ultrastructure, plastid arrangement and auxosporulation are described for Seminavis and resemble those in the Naviculaceae sensu stricto.     

Parastrombidinopsis minima n. sp. (Ciliophora: Oligotrichia) from the Coastal Waters of Northeastern Taiwan: Morphology and Small Subunit Ribosomal DNA Sequence

ABSTRACT. Parastrombidinopsis minima n. sp. is investigated, using live observations, protargol preparations, and molecular data. In living cells, the ranges of cell length are 85–95 μm, cell width 60–70 μm, and oral diameter 40–50 μm. In protargol‐impregnated specimens, cell length ranges between 43 and 71 μm, cell width between 23 and 42 μm, and oral diameter between 13 and 24 μm. The numbers of external oral polykinetids are 12–16 and of somatic kineties are 11–13. There are always two ovoid macronuclei (9–16 × 4–9 μm). Based on the analysis of morphologic data, the new species can be placed in the family Strombidinopsidae, but based on the small subunit rRNA gene sequence data, the Parastrombidinopsis species are more closely associated with strobilidiids and tintinnids.     

Spirotontonia taiwanica n. sp. (Ciliophora: Oligotrichida) from the Coastal Waters of Northeastern Taiwan: Morphology and Nuclear Small Subunit rDNA Sequence

ABSTRACT. The marine oligotrichous ciliate Spirotontonia taiwanica n. sp. isolated from the coastal waters of northeastern Taiwan is reported, using live observation, protargol preparations and molecular data. The new species differs from the most similar, known congener Spirotontonia turbinata in the following features: (1) lower number of buccal membranelles (11–13 vs. 13–17); (2) higher number of whorls of girdle kinety (2.5 vs. 1.5); (3) lower number of macronuclear nodules (20–31 vs. 28–40); (4) larger cell size (80–104 × 40–72 vs. 44–75 × 29–56 μm); (5) larger anterior cell end to buccal vertex (50 vs. 33 μm); (6) larger ratio of cell length to cell width (1.74 vs. 1.38); (7) the different beginning of the girdle kinety (posterior to the buccal vertex vs. left of the buccal zone portion); and (8) the disappearance of the L‐shaped argyrophilic structures in the last half whorl and occasionally the first 1–10 dikinetids (i.e. yes vs. no). The molecular data also reveal two distinct species, deviating by 2% or 33% base pairs.     

Vitis seeds (Vitaceae) from the late Neogene Gray Fossil Site, northeastern Tennessee, U.S.A.

This study focuses on morphometric and systematic analyses of the fossil Vitis seeds, recovered from the Gray Fossil Site (7-4.5 Ma, latest Miocene-earliest Pliocene), northeastern Tennessee, U.S.A. A multivariate analysis based on eleven measured characters from 76 complete fossil seeds recognizes three morphotaxa. Further comparisons with both selected modern and fossil vitaceous specimens confirm that these morphotaxa represent three new species, viz. Vitis grayensis sp. nov., Vitis lanatoides sp. nov., and Vitis latisulcata sp. nov. Furthermore, the close resemblance of the first two fossil grapes (V.grayensis and V.lanatoides) with two East Asian Vitis species provides further support concerning a strong eastern Asian aspect of the Gray fossil biota in the late Neogene southeastern North America, as previously evidenced by both animals (e.g. Pristinailurus bristoli [red panda]) and other plants (e.g. Sinomenium and Sargentodoxa).     

Extracellular Matrix Assembly in Diatoms (Bacillariophyceae) (I. A Model of Adhesives Based on Chemical Characterization and Localization of Polysaccharides from the Marine Diatom Achnanthes longipes and Other Diatoms)

Extracellular adhesives from the diatoms Achnanthes longipes, Amphora coffeaeformis, Cymbella cistula, and Cymbella mexicana were characterized by monosaccharide and methylation analysis, lectin-fluorescein isothiocyanate localization, and cytochemical staining. Polysaccharide was the major component of adhesives formed during cell motility, synthesis of a basal pad, and/or production of a highly organized shaft. Hot water-insoluble/hot 0.5 M NaHCO3-soluble anionic polysaccharides from A. longipes and A. coffeaeformis adhesives were primarily composed of galactosyl (64-70%) and fucosyl (32-42%) residues. In A. longipes polymers, 2,3-, t-, 3-, and 4-linked/substituted galactosyl, t-, 3-, 4-, and 2-linked fucosyl, and t- and 2-linked glucuronic acid residues predominated. Adhesive polysaccharides from C. cistula were EDTA-soluble, sulfated, consisted of 83% galactosyl (4-, 4,6-, and 3,4-linked/substituted) and 13% xylosyl (t-, 4f/5p-, and 3p-linked/substituted) residues, and contained no uronosyl residues. Ulex europaeus agglutinin uniformly localized [alpha](1,2)-L-fucose units in C. cistula and Achnanthes adhesives formed during motility and in the pads of A. longipes. D-Galactose residues were localized throughout the shafts of C. cistula and capsules of A. coffeaeformis. D-Mannose and/or D-glucose, D-galactose, and [alpha](t)-L-fucose residues were uniformly localized in the outer layers of A. longipes shafts by Cancavalia ensiformis, Abrus precatorius, and Lotus tetragonolobus agglutinin, respectively. A model for diatom cell adhesive structure was developed from chemical characterization, localization, and microscopic observation of extracellular adhesive components formed during the diatom cell-attachment process.     

Further Consideration of the Phylogeny of Some Traditional Heterotrichs (Protista, Ciliophora) of Uncertain Affinities, Based on New Sequences of the Small Subunit rRNA Gene

ABSTRACT. The systematic relationships and taxonomic positions of the traditional heterotrich genera Condylostentor, Climacostomum, Fabrea , Folliculina, Peritromus , and Condylostoma , as well as the licnophorid genus Licnophora , were re-examined using new data from sequences of the gene coding for small subunit ribosomal RNA. Trees constructed using distance-matrix, Bayesian inference, and maximum-parsimony methods all showed the following relationships: (1) the traditional heterotrichs consist of several paraphyletic groups, including the current classes Heterotrichea, Armophorea and part of the Spirotrichea; (2) the class Heterotrichea was confirmed as a monophyletic assemblage based on our analyses of 31 taxa, and the genus Peritromus was demonstrated to be a peripheral group; (3) the genus Licnophora occupied an isolated branch on one side of the deepest divergence in the subphylum Intramacronucleata and was closely affiliated with spirotrichs, armophoreans, and clevelandellids; (4) Condylostentor , a recently defined genus with several truly unique morphological features, is more closely related to Condylostoma than to Stentor ; (5) Folliculina, Eufolliculina , and Maristentor always clustered together with high bootstrap support; and (6) Climacostomum occupied a paraphyletic position distant from Fabrea , showing a close relationship with Condylostomatidae and Chattonidiidae despite of modest support.     

Evolution of the Hong Kong influenza A sub-type. Structural relationships between the haemagglutinin from A/duck/Ukraine/1/63 (Hav 7) and the Hong Kong (H3) haemagglutinins.

The relationship between the haemagglutinin from the influenza virus A/duck/Ukraine/1/63 (Hav 7) and the human Hong Kong variants (H3) has been investigated. Amino-acid-sequence analysis shows that the Hav 7 haemagglutinin closely resembles the 1968 human H3 haemagglutinin in structure. However, the number of amino-acid-sequence differences (23) suggest that the Hong Kong haemagglutinin gene did not come directly from A/duck/Ukraine/1/63 but from a virus derived from it by antigenic drift during the period 1963-1968.     

Subunit IV (Mr = 14,384) of the cytochrome b-c1 complex from Rhodobacter sphaeroides. Cloning, DNA sequencing, and ubiquinone binding domain.

The Rhodobacter sphaeroides gene encoding subunit IV of the cytochrome b-c1 complex (fbcQ) was cloned and sequenced. The fbcQ cistron is 372 base pairs long and encodes 124 amino acid residues. The molecular mass of subunit IV, deduced from the nucleotide sequence, is 14,384 Da. A hydropathy plot of the predicted amino acid sequence revealed only one transmembrane helix; it is near the C-terminal end. The 3-azido-2-methyl-5-methoxy-6-(3,7-dimethyl[3H]octyl)-1,4-benzoquinone ([3H]azido-Q)-labeled subunit IV was isolated from the [3H]-azido-Q-treated cytochrome b-c1 complex. A ubiquinone-binding peptide was obtained by digesting the labeled subunit IV with V8 protease followed by high performance liquid chromatography separation. Amino acid analysis and partial N-terminal sequencing of this ubiquinone-binding peptide revealed that it corresponded to residues 77-124 of subunit IV. Based on the hydropathy profile and predicted tendency to form alpha-helices and beta-sheets, we propose a structural model for subunit IV. In this model the ubiquinone-binding domain is located near the surface of the membrane.     

Fossil leaves of Buxus (Buxaceae) from the Upper Pliocene of Yunnan,SW China

A new species, Buxus pliosinica H.S. Huang, T. Su et Z.K. Zhou n. sp. (Buxaceae) is designated based on leaf architecture and cuticular features of five compressed fossil leaves from the Upper Pliocene Sanying Formation of Yunnan, SW China. Leaves of B. pliosinica are elliptic and small, with entire margin, retuse tip, intramarginal vein, and exmedially ramified tertiary veins. The leaves are hypostomatic with anomocytic stomatal apparatuses and giant stomata. Based on comparisons of leaf morphological and cuticular features, B. sempervirens Linnaeus is considered as the nearest living relative of B. pliosinica. Morphologically, these species share similar elliptic shape and size, cuneate base, retuse tip, similar ranges of petiole length, angles of 2° vein to midvein, and distance from the intramarginal vein to the margin. In terms of cuticular features, they are similar in type of stomatal apparatus, maximum length of giant stomata and range of stomatal length, but differ in the presence of indumentum. This discovery represents the first fossil record of Buxus from the SE margin of the Tibetan Plateau, and confirms the existence of Buxus in this region by the late Pliocene. Meanwhile, the newly described fossil species contributes to our understanding of the evolution of extant Buxus.     

A New Fossil of Necrotauliidae (Insecta: Trichoptera) from the Jiulongshan Formation of China and Its Taxonomic Significance

Background

Acisarcuatus variradius gen. et sp. nov., an extinct new species representing a new genus, is described from the Middle Jurassic Jiulongshan Formation in Daohugou Village, Inner Mongolia, China.

Methodology/Principal Findings

In this paper, we revised the diagnosis of Necrotauliidae Handlirsch, 1906. One new genus and species of Necrotauliidae is described. An analysis based on the fossil morphological characters clarified the taxonomic status of the new taxa.

Conclusions/Significance

New fossil evidence supports the viewpoint that the family Necrotauliidae belongs to the Integripalpia.