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  • 1
    Electronic Resource
    Electronic Resource
    Higher-Order Phylogeny of Plasmodial Slime Molds (Myxogastria) Based on Elongation Factor 1-A and Small Subunit rRNA Gene Sequences (2005)
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Abstract. The Myxogastria are common soil microorganisms with a life cycle comprised of a plasmodial trophic stage and large fruiting bodies generally visible with the unaided eye. Until now, their classification has been based exclusively on a combination of morphological, ultrastructural, and developmental characters. Our study is the first attempt to examine phylogenetic relationships among these taxa using molecular data. Partial small-subunit ribosomal RNA and/or elongation factor 1-alpha gene sequences were obtained from eleven, mostly field-collected species representing the five orders of Myxogastria. Nineteen sequences were obtained and subjected to phylogenetic analysis together with 10 sequences available from GenBank. Separate and combined analyses of the two data sets support the division of Myxogastria into three distinct groups. The most basal clade consists of the Echinosteliales, an order considered to have affinities with Protostelia. The three species examined possess unpigmented or slightly pigmented spores. The second group consists of Liceales and Trichiales, taxa characterized by the presence of clear, but pigmented, spores. The third group consists of the two remaining orders, Physarales and Stemonitales, both possessing dark spores. This suggests that spore pigmentation is an evolutionarily conservative character in myxogastrians, and that the simple morphology of echinostelids is not a derived feature.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.00032.x
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  • 2
    Electronic Resource
    Electronic Resource
    How many novel eukaryotic “kingdoms”? Pitfalls and limitations of environmental DNA surveys (2005)
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Over the past few years, the use of cultivation-independent techniques to detect eukaryotic diversity has proven to be a powerful approach. Based on small-subunit ribosomal RNA (SSU rRNA) gene analyses, these studies have revealed the existence of an unexpected variety of new phylotypes. Some of them do not seem to be related to any molecularly described lineage, and have been proposed to represent novel eukaryotic kingdoms. In order to critically review the evolutionary importance of this novel high-level eukaryotic diversity and to test the potential technical and analytical pitfalls and limitations of eukaryotic environmental DNA surveys (EES), we analysed 484 environmental SSU rRNA gene sequences, including 81 new sequences from sediments of the river Seymaz (Geneva, Switzerland). Based on a detailed screening of an exhaustive alignment of SSU rRNA gene sequences and the phylogenetic re-analysis of previously published sequences using Bayesian methods, our results suggest that the number of novel higher-level taxa revealed by previous EES was over-estimated. Three main sources of errors are responsible for this situation, namely (1) the presence of undetected chimeric sequences; (2) the misplacement of several fast evolving sequences; and (3) the incomplete sampling of described, but yet unsequenced eukaryotes. EES undoubtedly contribute to unravel many novel eukaryotic lineages, but there is no clear evidence for a spectacular increase of the diversity at a megaevolutionary level. After our re-analysis, we found only five candidate lineages of possible novel high-level eukaryotic taxa. To ascertain their taxonomic status, however, the organisms themselves have to be identified now.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_10.x
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  • 3
    Electronic Resource
    Electronic Resource
    A molecular perspective on the phylogeny of amoeboid protists (2005)
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The origin of amoeboid protists is one of the greatest enigmas of eukaryotic phylogeny. Although it has long been accepted that amoeboid protists are polyphyletic, the lack of molecular data for many amoeboid taxa impeded their placement in the tree of life. We have sequenced the small-subunit ribosomal RNA and actin genes from a broad taxonomic sampling of amoeboid protists, including three lineages of heliozoans (Actinophryida, Desmothoracida, and Taxopodida) and one lineage of radiolarians (Phaeodarea) for which no molecular data were available yet. Phylogenetic analyses of our data show that (1) all lobose amoebae sequenced to date belong to the recently defined phylum Amoebozoa and (2) Heliozoa and Radiolaria both represent polyphyletic assemblages, as suggested by previous ultrastructural studies. However, although axopodia evolved at least five times independently during the evolution of eukaryotes, our study also reveals that most protists possessing filopodia, reticulopodia, and/or axopodia are closely related, and constitute a new supergroup of amoeboid protists, the Rhizaria.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_11.x
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  • 4
    Electronic Resource
    Electronic Resource
    The twilight of sun-animalcules (2005)
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Molecular sampling of the taxonomic diversity of the living world is nowadays a task of paramount importance. Heliozoa represents one of the major eukaryotic taxa, which remain significantly underrepresented in molecular databases. The term Heliozoa was coined to embrace organisms with a rounded body and stiff pseudopodia. Despite evidences from ultrastructural studies, which conclusively show the polyphyly of selected heliozoan groups, contemporary morphological systems retain Heliozoa as a monophyletic taxon. From the perspective of reconstructing the true phylogeny of Eukaryota, molecular approaches to analyse relationships within this large protist group are evidently necessary. Phylogenetic analysis of our data shows that the four heliozoan taxa branch either independently or within different eukaryotic phyla. The actinophryids (Actinosphaerium, Actinophrys) appear as a lineage of stramenopiles, while the desmothoracids (Clathrulina, Hedriocystis) branch within “core Cercozoa”. The position of both groups is strongly supported in all analyses and is congruent with ultrastructure-based taxonomic revisions. The centrohelids (Chlamydaster, Heterophrys, Pterocystis, and Raphidiophrys) do not seem to be related to any particular eukaryotic phylum, in agreement with a recent molecular study. The taxopodid Sticholonche was found to branch between Polycystinea and Acantharea, two classes of radiolarians. Results obtained in this study suggest that the heliozoan body form cannot be used as a diagnostic argument to unite Heliozoa. Instead, we discriminate between the three heliomorphic taxa of independent origin, Actinophryida, Desmothoracida and Sticholonche, and propose the novel higher rank taxon Centrohelida. The term Heliozoa should thus be used solely in historical context.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_63.x
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  • 5
    Electronic Resource
    Electronic Resource
    Phylogeny of lobose amoebae based on actin and small-subunit ribosomal RNA genes (2005)
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: Lobose amoebae are abundant free-living protists and important pathogenic agents, yet their evolutionary history and position in the universal tree of life are poorly known. Molecular data for lobose amoebae are limited to a few species, and all phylogenetic studies published so far lacked representatives of many of their taxonomic groups. Here we analyse actin and small-subunit ribosomal RNA (SSU rRNA) gene sequences of a broad taxon sampling of naked, lobose amoebae. Our results support the existence of a monophyletic Amoebozoa clade, which comprises all lobose amoebae examined so far, as well as the amitochondriate pelobionts and entamoebids, and the slime molds. Both actin and SSU rRNA phylogenies distinguish two well-defined clades of amoebae, the “Gymnamoebia sensu stricto” and the Archamoebae (pelobionts+entamoebids), and one weakly supported and ill-resolved group comprising some naked, lobose amoebae and the Mycetozoa.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_26.x
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  • 6
    Electronic Resource
    Electronic Resource
    Small subunit ribosomal RNA sequences of Phaeodarea challenge the monophyly of Haeckel's Radiolaria (2005)
    Oxford, UK : Blackwell Science Inc
    The @journal of eukaryotic microbiology 52 (2005), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: In his grand monography of Radiolaria, Ernst Haeckel originally placed Phaeodarea within the class Radiolaria, together with Acantharea and Polycystinea. Cytological and ultrastructural studies, however, questioned the monophyly of Radiolaria, suggesting the independent evolutionary origin of the three taxa. Some recent molecular analyses based on small subunit ribosomal RNA (SSU rRNA) sequences challenged this classification, supporting the sisterhood of Acantharea and Polycystinea. In order to further test the monophyly of all Haeckel's Radiolaria, and as no data on Phaeodarea were available, we sequenced the complete SSU rRNA gene of three Phaeodarea and three Polycystinea. Our analyses show that the monophyletic Phaeodarea clearly branch among Cercozoa, and confirm that Acantharea and Polycystinea share a common history. This result enhances the morphological variability within Cercozoa, a phylum already containing very heterogeneous groups of protists. Our study suggests that the ability to secrete SrSO4 and the organization of microtubules inside axopodia are better phylogenetic markers than the simple presence of a central capsule and axopodia.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2005.05202003_1_66.x
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  • 7
    Electronic Resource
    Electronic Resource
    Sequence variations in the large-subunit ribosomal RNA gene of ammonia (foraminifera, protozoa) and their evolutionary implications (1996)
    Springer
    Journal of molecular evolution 43 (1996), S. 145-151 
    Details
    ISSN: 1432-1432
    Keywords: Foraminifera ; Sequence dissimilarity ; LSU rRNA gene ; Phylogeny
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract An unusually high divergence was observed in the ribosomal RNA genes of a free-living population of foraminifera belonging to the genusAmmonia. The sequences of a large-subunit (LSU) rDNA expansion segment D1 and flanking regions were obtained from 20 specimens namedAmmonia sp. 1 andAmmonia sp. 2. The sequence divergence between the two species averages 14%. Within each species it ranges from 0.2% to 7.1% inAmmonia sp. 1 and from 0.7% to 2.3% inAmmonia sp. 2. We did not find two specimens having identical sequences. Moreover, in opposition to the generally acaepted view, rDNA sequence variations were also found within a single individual. The variations among several rDNA copies in a single specimen ofAmmonia may reach up to 4.9%. Most of the observed variations result from multiplication of CA or TA serial repeats occurring in two particularly variable regions. For single base changes, C-T transitions are most frequently observed. We discuss the evolution of expansion segments and their use for phylogenetic studies.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02337359
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  • 8
    Electronic Resource
    Electronic Resource
    Phylogeny and Rates of Molecular Evolution of Planktonic Foraminifera: SSU rDNA Sequences Compared to the Fossil Record (1997)
    Springer
    Journal of molecular evolution 45 (1997), S. 285-294 
    Details
    ISSN: 1432-1432
    Keywords: Key words: Planktonic foraminifera — Molecular phylogenetics — Rates of substitution — Ribosomal DNA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract. Planktonic foraminifera are marine protists, whose calcareous shells form oceanic sediments and are widely used for stratigraphic and paleoenvironmental analyses. The fossil record of planktonic foraminifera is compared here to their molecular phylogeny inferred from ribosomal DNA sequences. Eighteen partial SSU rDNA sequences from species representing all modern planktonic families (Globigerinidae, Hastigerinidae, Globorotaliidae, Candeinidae) were obtained and compared to seven sequences representing the major groups of benthic foraminifera. The phylogenetic analyses indicate a polyphyletic origin for the planktonic foraminifera. The Candeinidae, the Globorotaliidae, and the clade Globigerinidae + Hastigerinidae seem to have originated independently, at different epochs in the evolution of foraminifera. Inference of their relationships, however, is limited by substitution rates of heterogeneity. Rates of SSU rDNA evolution vary from 4.0 × 10−9 substitutions/site/year in the Globigerinidae to less than 1.0 × 10−9 substitutions/site/year in the Globorotaliidae. These variations may be related to different levels of adaptation to the planktonic mode of life. A clock-like evolution is observed among the Globigerinidae, for which molecular and paleontological data are congruent. Phylogeny of the Globorotaliidae is clearly biased by rapid rates of substitution in two species (G. truncatulinoides and G. menardii). Our study reveals differences in absolute rates of evolution at all taxonomic levels in planktonic foraminifera and demonstrates their effect on phylogenetic reconstructions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00006232
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  • 9
    Electronic Resource
    Electronic Resource
    Molecular and morphological differentiation between species of the Plagiorchis vespertilionis group (Digenea, Plagiorchiidae) occurring in European bats, with a re-description of P. vespertilionis (Müller, 1780) (2000)
    Springer
    Systematic parasitology 47 (2000), S. 9-22 
    Details
    ISSN: 1573-5192
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract The taxonomic history of the species of Plagiorchis Lühe, 1899 occurring in European bats has been very confused because of high morphological similarity between different forms/species and the inadequate initial description of P. vespertilionis(Müller, 1780). As morphological data alone have not provided enough convincing arguments to solve the problem, the sequences from the nuclear rDNA ITS region (ITS1, 5.8S and ITS2) of three species of the P. vespertilionis group (P. vespertilionis, P. muelleri Tkach & Sharpilo, 1990 and P. koreanus Ogata, 1938) occurring in European bats were used to test the validity of these species and evaluate some of the morphological characters used for the species differentiation within this group. P. elegans from birds was used as the outgroup in the analysis. All three ingroup species were clearly distinguishable using ITS sequences. Among them, P. koreanus occupied a basal position, while P. vespertilionis and P. muelleri appeared as a cluster of two closely related, derived species. ITS sequences of the specimens obtained from different hosts and/or geographical areas did not exhibit any intraspecific variability. Morphological study of the material in collections revealed characters which enable the species of Plagiorchis from bats in Europe to be distinguished. Taking into account that the type-material of P. vespertilionis, described during the 18th Century, has been lost, for nomenclatural stability, a neotype is established and described. An amended description of the type-material of P. muelleri and keys for the determination of Plagiorchis spp. from European bats are presented.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1006358524045
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  • 10
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    Toxisarcon taimyr sp. nov., a new large monothalamous foraminifer from the Kara Sea inner shelf (2014)
    Springer
    In:  Marine Biodiversity, 44 (2). pp. 213-221.
    Details
    Publication Date: 2015-04-23
    Description: A large monothalamous foraminiferan, Toxisarcon taimyr sp. nov., has been isolated from the benthic samples from the Kara Sea inner shelf near the mouth of Yenisey river estuary, at a depth of 50–100 m. In its overall morphology, the new species closely resembles T. synsuicidica, one of the two species of Toxisarcon described to date. It possesses a large irregularly shaped cell body, covered by a thin layer of a fibrous organic coating. Numerous reticulopodia typically extend from all over the cell surface; the species is very motile and rapidly changes cell shape. Long and thick reticulopodial bundles form in the direction of movement. In the phylogenetic tree based on partial small-subunit ribosomal DNA (SSU rDNA) sequences, T. taimyr branches together with the two other known species of Toxisarcon within the clade C of monothalamous foraminifera.
    Type: Article , PeerReviewed
    Format: text
    DOI: 10.1007/s12526-014-0204-9
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    OceanRep: Article in a Scientific Journal - peer-reviewed
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