Phylogenetic Position of the Phacotaceae Within the Chlamydophyceae as Revealed by Analysis of 18S rDNA and rbcL Sequences

Four genera of the Phacotaceae (Phacotus, Pteromonas, Wislouchiella, Dysmorphococcus), a family of loricated green algal flagellates within the Volvocales, were investigated by means of transmission electron microscopy and analysis of the nuclear encoded small-subunit ribosomal RNA (18S rRNA) genes and the plastid-encoded rbcL genes. Additionally, the 18S rDNA of Haematococcus pluvialis and the rbcL sequences of Chlorogonium elongatum, C. euchlorum, Dunaliella parva, Chloromonas serbinowii, Chlamydomonas radiata, and C. tetragama were determined. Analysis of ultrastructural data justified the separation of the Phacotaceae into two groups. Phacotus, Pteromonas, and Wislouchiella generally shared the following characters: egg-shaped protoplasts, a single pyrenoid with planar thylakoid double-lamellae, three-layered lorica, flagellar channels as part of the central lorica layer, mitochondria located in the central cytoplasm, lorica development that occurs in mucilaginous zoosporangia that are to be lysed, and no acid-resistant cell walls. Dysmorphococcus was clearly different in each of the characters mentioned. Direct comparison of sequences of Phacotus lenticularis, Pteromonas sp., Pteromonas protracta, and Wislouchiella planctonica revealed DNA sequence homologies of ≥98.0% within the 18S gene and 93.9% within the rbcL gene. D. globosus was quite different from these species, with a maximum of 92.9% homology in the 18S rRNA and ≤86.6% in the rbcL gene. It showed major similarities to the 18S rDNA of Dunaliella salina, with 95.3%, and to the rbcL sequence of Chlamydomonas tetragama, with 90.3% sequence homology. Additionally, the Phacotaceae sensu stricto exclusively shared 10 (rbcL: 4) characters which were present neither in other Chlamydomonadales nor in Dysmorphococcus globosus. Different phylogenetic analysis methods confirmed the hypothesis that the Phacotaceae are polyphyletic. The Phacotaceae sensu stricto form a stable cluster with affinities to the Dunaliellaes and possibly Haematococcus pluvialis. Dysmorphococcus globosus represented an independent lineage that is possibly related to Chlamydomonas moewusii and C. tetragama. Received: 9 June 1997 / Accepted: 17 October 1997     

Developmental studies on the loricate choanoflagellate Stephanoeca diplocostata Ellis. III. Growth and turnover of silica,preliminary observations

Growth, turnover of silica and lorica morphology of Stephanoeca diplocostata Ellis have been investigated in batch cultures at 20 °C. Mean cell doubling times for separate experiments ranged from 9.1–13.8 h. During exponential growth, uptake of reactive silicate progressed steadily and throughout this phase the average amount of biogenic silicon per cell was 2.1 pg. Once growth declined, net dissolution of silica from loricae became apparent and progressed steadily throughout the stationary and death phases. The minor difference in solubility between loricae of living cells and costal strips cleaned with acid indicates that even if an organic component is associated with the silica of costal strips it does not inhibit silica dissolution. The first effects of silica dissolution on cells as revealed by electron microscopy are limited to corrosion on the surfaces and the hollowing out of the centres of costal strips but ultimately a consistent pattern of lorica disintegration occurs.     

西江颗粒直链藻种群生态特征

西江肇庆段是珠江干流汇入珠三角河网水域的咽喉通道,结合长期定点连续采样和空间季节性调查,重点对2009年西江干流肇庆段的颗粒直链藻(Aulacoseira granulata)的种群生态学特征进行系统分析。结果显示:全年中,颗粒直链藻在总种群中所占百分比均值为25.37%,与总种群丰度存在极显著正相关关系,这表明颗粒直链藻是西江浮游植物群落的重要优势种。调查期间发现了颗粒直链藻的4种形态,包括原变种(var.granulata)、极狭变种(var.angustissima)、弯曲变种(var.curvata)和极狭变种螺旋变型(var.angustissima f.spiralis)。其中,原变种占有绝对优势地位,其相对百分组成的年均值为91.47%,推测为原变种的形态结构比其它3种形态更容易适应外界环境变化,进而形成优势群体。颗粒直链藻总密度的周年变化呈现明显的双峰型,两个峰值分别出现在8月和11月,主要得益于适宜的水温、相对稳定的水体和较高的营养盐水平,这些均有助于颗粒直链藻的生长繁殖。第一个高峰之前,颗粒直链藻总密度未出现明显的波动,这很可能是由于水体径流量增大导致的稀释作用和频繁降雨导致的水体剧烈波动对颗粒直链藻增长的负作用掩盖了水温上升所带来的益处。从空间分布来看,颗粒直链藻总丰度的最大值一般出现在S1、S5和S6站点,这与营养盐最大值的空间分布格局是一致的。     

Phylogenetic position of a deep-sea ascidian, Megalodicopia hians, inferred from the molecular data

Ascidians inhabit both shallow water and the deep sea. The phylogenetic position of deep-sea ascidians has not been sufficiently investigated because of their unusual habitats. The family Octacnemidae is one such enigmatic deep-sea ascidian. In this report, we determined the sequences of the 18SrDNA and a mitochondrial protein gene of Megalodicopia hians belonging to the family Octacnemidae, and we analyzed its phylogenetic relationship with other ascidians. A phylogenetic relationship of this family with the families Cionidae and/or Corellidae has been suspected based on a small number of morphological characteristics. However, our results suggested that M. hians has a close relationship to the family Corellidae and might originate from them. This is the first report of the molecular phylogenetic analysis of a deep-sea ascidian.     

Lagenophrys anticthos N. Sp. and L. aegleae Mouchet-Bennati, 1932 (Ciliophora,Peritricha, Lagenophryidae), Ectocommensals of South American Crustaceans1

ABSTRACT. Lagenophrys anticthos n. sp. resembles L. aegleae Mouchet-Bennati; however, the two species are distinguished from one another by differences in the structure of the lorica aperture. Similarities in the shape of the lorica and macronucleus indicate a close phylogenetic relationship between L. anticthos and L. aegleae. The size of L. anticthos varies greatly within a population, and it is unclear whether this can be attributed to genetic differences or to environmental factors. In L. anticthos, variation in the form of the lips of the lorica aperture is correlated with variation in size. The brown, iron-rich incrustations observed around the loricae of L. aegleae by an earlier worker were not seen, indicating that the incrustations do not play a role in the symbiosis between L. aegleae and its host as was previously thought.     

1株近平滑假丝酵母的分离及其鉴定

采用平板稀释法从土壤及水果中分离出1株近平滑假丝酵母（Candida parapsilosis）,YPD培养基培养酵母,利用分子生物学方法对其rRNA基因内转录间区（ITS区）进行了克隆测序,并与GenBank中已有的有关序列进行比较及系统发育分析。测序结果表明该序列长度为547 bp,与GenBank中近平滑假丝酵母同源率在98.5%~100%之间,进化分析表明与C.parapsilosis（EF193067）、C.parapsilosis UOA/HCPF（FJ872013）属于一单独分支中,形态结果及分子鉴定表明近平滑假丝酵母培养成功,为其进一步开发利用提供了依据。     

Molecular phylogeny of hybridizing species from the genus Spartina Schreb. (Poaceae)

Interspecific hybridization events have been reported in the genus Spartina Schreb. (Poaceae), involving the east American species Spartina alterniflora, and including either introgression (e.g., with the western American Spartina foliosa) or allopolyploid speciation (e.g., with the Euro-African Spartina maritima). Molecular phylogenetic analysis of the genus has been undertaken in order to understand phylogenetic relationships and genetic divergence among these hybridizing species. Twelve Spartina species have been sequenced for two nuclear DNA regions (ITS of ribosomal DNA, and part of the Waxy gene) and one chloroplast DNA spacer (trnT-trnL). Separate and conditional combined phylogenetic analyses using Cynodon dactylon as the outgroup have been conducted. Spartina is composed of two lineages. The first clade includes all hexaploid species: the Euro-African S. maritima (2n = 60), the East-American S. alterniflora (2n = 62) and the West-American S. foliosa (2n = 60). Spartina alterniflora appears as a closely related sister species to S. foliosa. Although belonging to the same lineage, Spartina maritima appears consistently more genetically differentiated from S. alterniflora than S. foliosa. The tetraploid species S. argentinensis (2n = 40) is placed at the base of this first clade according to the Waxy data, but its position is not well resolved by the other sequences. The second well-supported main lineage within genus Spartina includes the other tetraploid American species. Significant incongruence has been encountered between the waxy based tree and both the ITS and trnT-trnL trees concerning the position of S. densiflora, suggesting a possible reticulate evolution for this species. The results agree with hybridization patterns occurring in Spartina: introgression involving closely related species (S. alterniflora and S. foliosa) on one hand, and alloploid speciation involving more differentiated species (S. alterniflora and S. maritima) on the other hand.     

Pollination biology, mating system, and seed set in a Danish population of Saxifraga granulata

Saxifraga granulata is able to reproduce both sexually and vegetatively. In an earlier report from Denmark, seed set was said to be low, the species reproducing mainly vegetatively by means of bulbils. Furthermore, investigations in northern England have shown inbreeding depression in gynodioecious 5. granulata populations. The present study, however, demonstrates that 5. granulata is fully self-compatible in Denmark; seed set per flower in hand-selfings was on average 70%, compared to ca. 80% in control plants. Nevertheless, despite high seed set, reproduction by bulbils is probably the most important mode of reproduction. Saxifraga granulata has typically opportunistic flowers which are white, UV-neutral compared to the background reflexion, and offering only a small standing crop of nectar. Optical attraction by the massive flowering over a relatively short period is regarded as a way of overcoming competition from co-occurring, simultaneously flowering species. Saxifraga granulata flowers received visits from at least 27 different insects species. Based on number of recorded flower visits, records on foraging time, and investigations of body surface pollen loads, Rhamphomyia sulcata (Empididae), Cheilosia spp. (Syrphidae), Polyblepharis opaca (Empididae), and Halictus spp. ( s. I .) (Halictidae) were found to be the most important pollen vectors in the 5. granulata population.     

Characterization of Bacteriophages Cp1 and Cp2, the Strain-Typing Agents for Xanthomonas axonopodis pv. citri

The strains of Xanthomonas axonopodis pv. citri, the causative agent of citrus canker, are historically classified based on bacteriophage (phage) sensitivity. Nearly all X. axonopodis pv. citri strains isolated from different regions in Japan are lysed by either phage Cp1 or Cp2; Cp1-sensitive (Cp1^s) strains have been observed to be resistant to Cp2 (Cp2^r) and vice versa. In this study, genomic and molecular characterization was performed for the typing agents Cp1 and Cp2. Morphologically, Cp1 belongs to the Siphoviridae. Genomic analysis revealed that its genome comprises 43,870-bp double-stranded DNA (dsDNA), with 10-bp 3′-extruding cohesive ends, and contains 48 open reading frames. The genomic organization was similar to that of Xanthomonas phage phiL7, but it lacked a group I intron in the DNA polymerase gene. Cp2 resembles morphologically Escherichia coli T7-like phages of Podoviridae. The 42,963-bp linear dsDNA genome of Cp2 contained terminal repeats. The Cp2 genomic sequence has 40 open reading frames, many of which did not show detectable homologs in the current databases. By proteomic analysis, a gene cluster encoding structural proteins corresponding to the class III module of T7-like phages was identified on the Cp2 genome. Therefore, Cp1 and Cp2 were found to belong to completely different virus groups. In addition, we found that Cp1 and Cp2 use different molecules on the host cell surface as phage receptors and that host selection of X. axonopodis pv. citri strains by Cp1 and Cp2 is not determined at the initial stage by binding to receptors.     

Antioxidant binding of caeruloplasmin to myeloperoxidase: Myeloperoxidase is inhibited,but oxidase,peroxidase and immunoreactive properties of caeruloplasmin remain intact

The neutrophil enzyme myeloperoxidase (MPO) purposefully makes hypochlorous acid (HOCl) as part of the cells defence against microbial infections. During cell lysis, however, MPO will be released into the extracellular environment where production of HOCl, a powerful oxidant, will lead to molecular damage. Extracellular MPO binds to the copper-containing protein caeruloplasmin (Cp) and prevents MPO making HOCl. Cp has several important antioxidant functions in extracellular fluids associated with its ability to catalyse oxidation of ferrous ions and to remove peroxides. The binding of MPO to Cp did not inhibit these important extracellular antioxidant activities of Cp, but in so doing it provided additional antioxidant protection against formation of HOCl.     

Antioxidant binding of caeruloplasmin to myeloperoxidase: myeloperoxidase is inhibited, but oxidase, peroxidase and immunoreactive properties of caeruloplasmin remain intact

The neutrophil enzyme myeloperoxidase (MPO) purposefully makes hypochlorous acid (HOCl) as part of the cells defence against microbial infections. During cell lysis, however, MPO will be released into the extracellular environment where production of HOCl, a powerful oxidant, will lead to molecular damage. Extracellular MPO binds to the copper-containing protein caeruloplasmin (Cp) and prevents MPO making HOCl. Cp has several important antioxidant functions in extracellular fluids associated with its ability to catalyse oxidation of ferrous ions and to remove peroxides. The binding of MPO to Cp did not inhibit these important extracellular antioxidant activities of Cp, but in so doing it provided additional antioxidant protection against formation of HOCl.     

Phylogenetic autocorrelation and heritability of geographic range size,shape and position of fiddler crabs,genus Uca (Crustacea,Decapoda)

The aim of this study was to evaluate the levels of phylogenetic heritability of the geographical range size, shape and position for 88 species of fiddler crabs of the world, using phylogenetic comparative methods and simulation procedures to evaluate their fit to the neutral model of Brownian motion. The geographical range maps were compiled from literature, and range size was based on the entire length of coastline occupied by each species, and the position of each range was calculated as its latitudinal and longitudinal midpoint. The range shape of each species was based in fractal dimension (box‐counting technique). The evolutionary patterns in the geographical range metrics were explored by phylogenetic correlograms using Moran’s I autocorrelation coefficients, autoregressive method (ARM) and phylogenetic eigenvector regression (PVR). The correlograms were compared with those obtained by simulations of Brownian motion processes across phylogenies. The distribution of geographical range size of fiddler crabs is right‐skewed and weak phylogenetic autocorrelation was observed. On the other hand, there was a strong phylogenetic pattern in the position of the range (mainly along longitudinal axis). Indeed, the ARM and PVR evidenced, respectively, that ca. 86% and 91% of the longitudinal midpoint could be explained by phylogenetic relationships among the species. The strong longitudinal phylogenetic pattern may be due to vicariant allopatric speciation and geographically structured cladogenesis in the group. The traits analysed (geographical range size and position) did not follow a Brownian motion process, thus suggesting that both adaptive ecological and evolutionary processes must be invoked to explain their dynamics, not following a simple neutral inheritance in the fiddler‐crab evolution.     

Ceruloplasmin,a copper-transport protein,can act as a growth promoter for some cell lines in serum-free medium

Summary Ceruloplasmin (Cp) is a copper-transport protein with ferric oxidase activity found in high concentrations in the plasma of all vertebrates. Five cell lines (TR-1, TR-M, TR-ST, TM₃, and TM₄) derived from the testis can be grown in hormone-supplemented serum-free medium. Cp stimulates the growth of four of these five cell lines in serum-free medium. The growth stimulation by Cp is not affected by the addition or deletion of free copper, nor does copper itself elicit any significant growth response. Cp can stimulate growth also in the absence of TF suggesting that it is not acting solely to promote Fe(III)-TF binding. A strong interaction is seen between Cp and high density lipoprotein (HDL), with the presence of either decreasing the growth-promoting activity of the other. It is suggested that these cell lines may provide an ideal system for studying the action of Cp at the cellular level. Presented in the symposium on Plant and Animal Physiology in Vitro at the 33rd Annual Meeting of the Tissue Culture Association, San Diego, California, June 6–10, 1982. This work was supported by NIH P50 Grant HO-13541. I am grateful to Ms. Florence Kaczorowski for her expert technical assistance. This symposium was supported in part by the following organizations: Bellco Glass, Inc., California Branch of the Tissue Culture Association, Collaborative Research, Hana Media, Hybridtech, K C Biological, Inc., and Millipore Corporation.     

Neustonic Marine Craspedomonadales (Choanofiagellates) from Washington and California

SYNOPSIS. Neustonic choanoflagellates can be found in marine tide pools in the San Juan Islands, Washington, and on the Monterey Peninsula, California. Several marine photo-synthetic Chrysophyceae (in the Pedinellaceae), which also occur in these regions, have a basic structure so similar to choanoflagellates that this family is placed in the Craspedomonadales. In pointing out this relationship, the derivation of the Craspedomonadales from pigmented Chrysophyceae is strongly indicated.
In addition to the naked choanoflagellates, which are placed in the Codonosigaceae, these organisms produce loricae of two different types: 1) loricae possibly of cellulose and without visible structure in the light microscope (Salpingoecaceae), 2) loricae composed of silica strands, sometimes forming a mesh with large open spaces (Acanthoecaceae). Members of the latter family seem to be confined to a marine environment and are a prominent part of this investigation. Examination of several species with the electron microscope has revealed interesting details of lorica morphology that are not visible with the light microscope.
Several new combinations of taxa are proposed in addition to new taxa, including 4 new species of Salpingoeca , 3 new species of Diploeca and 4 new species of Pleurasiga. Three new genera are described, Ellisiella gen. nov., Acanthoecopsis gen. nov., and Sportelloeca gen. nov.     

Systematic position and phylogenetic relationships of the family Omphalometridae (Digenea, Plagiorchiida) inferred from partial lsrDNA sequences

The phylogenetic relationships and systematic position of the digenean genus Omphalometra Looss, 1899 and several other closely related genera, have always been controversial and opinions of different authors on the systematic rank and content of this group have varied greatly. Molecular analysis based on the partial sequences of the large subunit ribosomal DNA gene of representatives of the genera Omphalometra, Rubenstrema and Neoglyphe as well as previously published sequences of members of five families of Plagiorchioidea, has demonstrated: (1) close phylogenetic relationships between these three genera, and (2) a strong support of their position within the family Plagiorchiidae as a well-defined separate clade considered here as a subfamily Omphalometrinae. Molecular data do not support the close affinities of the members of Omphalometrinae and genus Opisthioglyphe as has been suggested by majority of previous authors. Among Omphalometrinae, Omphalometra flexuosa (a parasite of moles, Talpidae) occupies a basal position in relation to Rubenstrema exasperatum and Neoglyphe locellus (both parasitic in shrews, members of the more evolutionary advanced family Soricidae). An extremely low level of lsrDNA sequence divergence between Neoglyphe and Rubenstrema suggests very close phylogenetic relationships of these two genera. Results of the molecular analysis are briefly discussed in comparison with the previously published systems.     

Conflicting phylogenetic position of Schizosaccharomyces pombe

The phylogenetic position of the fission yeast Schizosaccharomyces pombe in the fungal Tree of Life is still controversial. Three alternative phylogenetic positions have been proposed in the literature, namely (1) a position basal to the Hemiascomycetes and Euascomycetes, (2) a position as a sister group to the Euascomycetes with the Hemiascomycetes as a basal branch, or (3) a sister group to the Hemiascomycetes with Euascomycetes as a basal branch. Here we compared 91 clusters of orthologous proteins containing a single orthologue that are shared by 19 eukaryote genomes. The major part of these 91 orthologues supports a phylogenetic position of S. pombe as a basal lineage among the Ascomycota, thus supporting the second proposition. Interestingly, part of the orthologous proteins supported a fourth, not yet described alternative, in which S. pombe is basal to both Basidiomycota and Ascomycota. Both topologies of phylogenetic trees are well supported. We believe that both reflect correctly the phylogenetic history of the species concerned. This apparent paradox may point to a heterogeneous nuclear genome of the fungi. Importantly, this needs to be taken in consideration for a correct understanding of the fungal Tree of Life.     

Methylation status of 13S ribosomal RNA from hamster mitochondria: the presence of a novel riboside, N4-methylcytidine.

The ribosomal RNA ("13S" RNA) of the small ribosomal subunit of hamster cell mitochondria has been found to have a distinctive pattern of methylated residues. Each molecule contained, on the average, approximately one residue of m4Cp, m5Cp and m5Up, and two residues of m62Ap. The natural occurrence of m4Cp has not previously been reported; we propose that this nucleotide is homologous to its ribose-methylated congener, m4Cmp, which is characteristic of bacterial 16S ribosomal RNA. We detected neither m4Cp nor m4Cmp in the hamster cell cytoplasmic ribosomal RNA. This is the first documentation of a modified residue present in mitochondrial RNA but absent from the cytoplasmic RNA of the same cells.     

Rasterelektronenmikroskopische und biometrische Untersuchungen über die Variabilität der Form, Struktur und Größe des Gehäuses einiger limnischer Tintinnina (Protozoa, Ciliophora)

The loricae of the fresh-water Tintinnina Codonella cratera, Tinitinnidium fluviatile , and Tintinnopsis cylindrata were investigated for their variability in shape, structure, and size, using scanning electron microscopy and variance analysis. The intrastrain variability of length and width of the loricae is significantly smaller than the interstrain variability. The shells are shorter in autumn than in spring. The lorica of C. cratera consists of biogenic and non-biogenic flakes, irregularly cemented by a substance which is released from the organism. Building of the shell is not restricted to the time of binary fission. T. fluviatile and T. cylindrata have soft and sticky loricae which are heavily agglutinated by various biogenic and non-biogenic particles. The material used for lorica-building and/or agglutination depends on environment and season. There is a relationship between the structure of the lorica and the degree of eutrophication in the lake. The significance of these findings for paleolimnology and taxonomy and the function of the lorica in fresh-water Tintinnina are discussed.     

Molecular phylogeny of the Australian frog genera Crinia, Geocrinia, and allied taxa (Anura: Myobatrachidae).

We present a mitochondrial gene tree for representative species of all the genera in the subfamily Myobatrachinae, with special emphasis on Crinia and Geocrinia. This group has been the subject of a number of long-standing taxonomic and phylogenetic debates. Our phylogeny is based on data from approximately 780 bp of 12S rRNA and 676 bp of ND2, and resolves a number of these problems. We confirm that the morphologically highly derived monotypic genera Metacrinia, Myobatrachus, and Arenophryne are closely related, and that Pseudophryne forms the sister group to these genera. Uperoleia and the recently described genus Spicospina are also part of this clade. Our data show that Assa and Geocrinia are reciprocally monophyletic and together they form a well-supported clade. Geocrinia is monophyletic and the phylogenetic relationships with the genus are fully resolved with two major species groups identified: G. leai, G. victoriana, and G. laevis; and G. rosea, G. alba, and G. vitellina (we were unable to sample G. lutea). We confirm that Taudactylus forms the sister group to the other myobatrachine genera, but our data are equivocal on the phylogenetic position of Paracrinia. The phylogenetic relationships among Crinia species are well resolved with strong support for a number of distinct monophyletic clades, but more data are required to resolve relationships among these major Crinia clades. Crinia tasmaniensis and Bryobatrachus nimbus form the sister clade to the rest of Crinia. Due to the lack of generic level synapomorphies for a Bryobatrachus that includes C. tasmaniensis, we synonymize Bryobatrachus with Crinia. Crinia georgiana does not form a clade distinct from other Crinia species and so our data do not support recognition of the genus Ranidella for other Crinia species. Crinia subinsignifera, C. pseudinsignifera, and C. insignifera are extremely closely related despite differences in male advertisement call. A preliminary investigation of phylogeographic substructure within C. signifera revealed significant divergence between samples from across the range of this species.