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  • 11
    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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  • 12
    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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  • 13
    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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  • 14
    Electronic Resource
    Electronic Resource
    Molecular Identification of Algal Endosymbionts in Large Miliolid Foraminifera: 1. Chlorophytes (2001)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 48 (2001), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: . Large miliolid foraminifers bear various types of algal endosymbionts including chlorophytes, dinoflagellates, rhodophytes, and diatoms. Symbiosis plays a key role in the adaptation of large foraminifera to survival and growth in oligotrophic seas. The identity and diversity of foraminiferal symbionts, however, remain largely unknown. In the present work we use ribosomal DNA (rDNA) sequences to identify chlorophyte endosymbionts in large miliolid foraminifera of the superfamily Soritacea. Partial 18S and complete Internal Transcribed Spacer (ITS) rDNA sequences were obtained from symbionts of eight species representing all genera of extant chlorophyte-bearing Soritacea. Phylogenetic analysis of the sequences confirms the previous fine structure-based identification of these endosymbionts as belonging to the genus Chlamydomonas. All foraminiferal symbionts form a monophyletic group closely related to Chlamydomonas noctigama. The group is composed of seven types identified in this study, including one previously morphologically described species, Chlamydomonas hedleyi. Each of these types can be considered as a separate species, based on the comparison of genetic differences observed between other established Chlamydomonas species. Several foraminiferal species share the same symbiont type, but only one species, Archaias angulatus, was found to bear more than one type.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.2001.tb00325.x
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  • 15
    Electronic Resource
    Electronic Resource
    The Life Cycle of Rotaliella elatiana N. Sp.: A Tiny Macroalgavorous Foraminifer from the Gulf of Elat (1992)
    Oxford, UK : Blackwell Publishing Ltd
    The @journal of eukaryotic microbiology 39 (1992), S. 0 
    Details
    ISSN: 1550-7408
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: . A new foraminiferan species, Rotaliella elatiana n. sp., was isolated in the Gulf of Elat, where it lives in association with a macrophytic green alga, Enteromorpha. The agamont of this tiny new species has a transparent test composed of a bilocular embryonic chamber followed by six to seven trochospirally coiled inflated chambers. The spiral sutures are undulated. The umbilical side has numerous denticules and has radial grooves. The gamont has only one inflated chamber. Rotaliella elatiana has a classical, heterophasic life cycle, with a regular alternation of diploid agamontic phase and haploid gamontic phase. The gamontic phase of the life cycle is exceptionally reduced and the uninucleated gamonts pair immediately after they build their first chamber. A few cases of autogamic reproduction were observed. R. elatiana is a heterocaryotic species; agamonts have one somatic and two to three generative nuclei.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1550-7408.1992.tb01293.x
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  • 16
    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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  • 17
    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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  • 18
    Electronic Resource
    Electronic Resource
    Naked foraminiferans revealed (1999)
    [s.l.] : Macmillan Magazines Ltd.
    Nature 399 (1999), S. 27-27 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] It is generally assumed that the first fossil appearance of a group of organisms corresponds to its evolutionary origin. But we have molecular evidence that extant members of the most abundant microfossil-forming group, the Foraminifera, include ‘naked’ amoeboid species, indicating ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/19881
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  • 19
    Electronic Resource
    Electronic Resource
    First insights into the biodiversity and biogeography of the Southern Ocean deep sea (2007)
    [s.l.] : Nature Publishing Group
    Nature 447 (2007), S. 307-311 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] Shallow marine benthic communities around Antarctica show high levels of endemism, gigantism, slow growth, longevity and late maturity, as well as adaptive radiations that have generated considerable biodiversity in some taxa. The deeper parts of the Southern Ocean exhibit some unique ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/nature05827
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  • 20
    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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