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Phylogenomic Insights into the Origin of Primary Plastids
No full textAbstract The origin of plastids was a major evolutionary event that paved the way for an astonishing diversification of photosynthetic eukaryotes. Plastids originated by endosymbiosis between a heterotrophic eukaryotic host and cyanobacteria, presumably in a common ancestor of the primary photosynthetic eukaryotes (Archaeplastida). A single origin of primary plastids is well supported by plastid evidence but not by nuclear phylogenomic analyses, which have consistently failed to recover the monophyly of Archaeplastida hosts. Importantly, plastid monophyly and nonmonophyletic hosts could be explained under scenarios of independent or serial eukaryote-to-eukaryote endosymbioses. Here, we assessed the strength of the signal for the monophyly of Archaeplastida hosts in four available phylogenomic data sets. The effect of phylogenetic methodology, data quality, alignment trimming strategy, gene and taxon sampling, and the presence of outlier genes were investigated. Our analyses revealed a lack of support for host monophyly in the shorter individual data sets. However, when analyzed together under rigorous data curation and complex mixture models, the combined nuclear data sets supported the monophyly of primary photosynthetic eukaryotes (Archaeplastida) and recovered a putative association with plastid-lacking Picozoa. This study represents an important step toward better understanding deep eukaryotic evolution and the origin of plastids. [Archaeplastida; Bayesian; chloroplast; maximum likelihood; mixture model; ortholog; outlier loci; paralog; protist.
Author Correction: A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids
No full textA molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids
Get PDFIn modern oceans, eukaryotic phytoplankton is dominated by lineages with red algal-derived plastids such as diatoms, dinoflagellates, and coccolithophores. Despite the ecological importance of these groups and many others representing a huge diversity of forms and lifestyles, we still lack a comprehensive understanding of their evolution and how they obtained their plastids. New hypotheses have emerged to explain the acquisition of red algal-derived plastids by serial endosymbiosis, but the chronology of these putative independent plastid acquisitions remains untested. Here, we establish a timeframe for the origin of red algal-derived plastids under scenarios of serial endosymbiosis, using Bayesian molecular clock analyses applied on a phylogenomic dataset with broad sampling of eukaryote diversity. We find that the hypotheses of serial endosymbiosis are chronologically possible, as the stem lineages of all red plastid-containing groups overlap in time. This period in the Meso- and Neoproterozoic Eras set the stage for the later expansion to dominance of red algal-derived primary production in the contemporary oceans, which profoundly altered the global geochemical and ecological conditions of the Earth
eine Analyse von Ultrastruktur, Phylogenie und Kospeziation
No full textThe complex mechanisms leading to a tripartite symbiosis involving bacteria,
flagellates, and host termites are not yet fully understood. While the
flagellates are known to play a major role in the degradation of the
cellulosic food of the termites, in most cases, the functions of the diverse
flagellate-associated bacteria are completely obscure. Unambiguous
identification of the mostly uncultivable prokaryotes and eukaryotes is an
important step in understanding the mutual interactions between the two
partners. For this purpose, in the studies described in my thesis,
morphological investigations (light microscopy and electron microscopy) were
combined with molecular phylogenetic analyses (full-cycle-rRNA approach). In
two earlier light microscopy studies, other authors reported contradicting
numbers of devescovinid flagellates occurring in the hindgut of the dry-wood
termite Incisitermes marginipennis. We clearly and unambiguously documented
the presence of only one devescovinid species (Metadevescovina modica)
inhabiting the gut of I. marginipennis using a combination of various light
and electron microscopy techniques and molecular phylogenetic analysis of the
small subunit (SSU) rRNA gene sequences. Moreover, we confirmed the validity
of the genus Metadevescovina, which had long been discussed as being the same
as the genus Devescovina; monophyly of each of the genera was revealed by
molecular phylogenetic analyses. Metadevescovina could not be distinguished
from Devescovina solely by morphological characteristics of the flagellates
themselves, but the two flagellate genera could be differentiated by examining
their bacterial symbionts. The cell surface of Metadevescovina flagellates is
densely colonized with spirochetes, and that of Devescovina flagellates is
densely covered with filamentous bacteria affiliated to the Bacteroidales.
Molecular phylogenetic analyses of Devescovina spp. and their bacterial
symbionts from a wide range of Kalotermitidae revealed that the termites
acquired two bacterial symbionts by two different routes: vertical
transmission and horizontal transmission. The ectosymbionts of Devescovina
spp. form a monophyletic group within the Bacteroidales (“Candidatus
Armantifilum devescovinae”). Congruence analyses of the phylogenetic trees of
Devescovina spp. and “Candidatus Armantifilum devescovinae” documented a
strict cospeciation of the partners, which indicated an obligate symbiosis,
leading to a vertical transmission of the bacteria within their host lineages.
The ‘Endomicrobia’ endosymbionts of Devescovina spp. are most closely related
to endosymbionts of phylogenetically unrelated termite gut flagellates, which
indicated that these symbionts were acquired by horizontal transmission
between different flagellate species present in the same termite gut. In a
further study documented in this thesis, the multiple symbionts of the
flagellate Joenia annectens from the dry-wood termite Kalotermes flavicollis
were identified, localized using a full-cycle-rRNA approach, and
morphologically described at the ultrastructural level. Two populations of J.
annectens could be distinguished not only by their SSU rRNA gene sequences
(0.8% sequence divergence), but also by differences in their assemblages of
bacterial symbionts. Each of the flagellate populations hosted
phylogenetically distinct ectosymbionts from the phylum Bacteroidetes, while a
single phylotype of ‘Endomicrobia’ was consistently associated with only one
of the host phylotypes. However, not all individuals were colonized, once
again corroborating that ‘Endomicrobia’ are not always cospeciating with their
host lineages. The results reported in my thesis provide important information
about the specificity of the symbioses between termite gut flagellates and
their bacterial symbionts. This information is necessary for further studies
of the function of these symbioses. A possible involvement of bacterial
symbionts in the nitrogen metabolism of the host flagellates is discussed.Die komplexen Mechanismen, welche der Dreiersymbiose zwischen Bakterien,
Flagellaten und ihren Wirtstermiten zugrundeliegen, sind bis heute noch
weitgehend unverstanden. Während den Flagellaten eine wesentliche Rolle beim
Abbau der cellulosehaltigen Nahrung der Termiten zugeschrieben wird, sind die
Funktionen der diversen, mit den Flagellaten assoziierten Bakterien in den
meisten Fällen komplett unbekannt. Ein wichtiger Schritt für die Erforschung
der wechselseitigen Beziehungen zwischen den in der Regel nicht kultivierbaren
pro- und eukaryotischen Symbionten stellt deren eindeutige Identifizierung
dar. Dazu wurden in den vorliegenden Studien morphologische Untersuchungen
(Licht- und Elektronenmikroskopie) beider Partner mit molekular-
phylogenetischen Analysen kombiniert (full-cycle-rRNA approach). In zwei
vorangegangenen lichtmikroskopischen Studien anderer Autoren wurde für die
Trockenholztermite Incisitermes marginipennis eine widersprüchliche
Artenanzahl von devescoviniden Flagellaten dokumentiert. Durch den Einsatz
verschiedener licht- und elektronenmikroskopischer Techniken sowie durch die
Analyse der Sequenzvariabilität der Gene der kleinen ribosomalen Untereinheit
(SSU rRNA) konnten wir in der vorliegenden Arbeit eindeutig zeigen, dass I.
marginipennis lediglich eine Art devescovinider Flagellaten (Metadevescovina
modica) im Darm beherbergt. Gleichzeitig konnten wir die Gültigkeit der
Gattung Metadevescovina, welche bis zum heutigen Tag stark umstritten war und
häufig als Synonym zu Devescovina angesehen wurde, bestätigen.
Molekularphylogenetische Analysen zeigten, dass beide Gattungen jeweils eine
separate monophyletische Gruppe bilden. Eine Unterscheidung der beiden
Gattungen an Hand morphologischer Merkmale der Flagellaten selbst war nicht
möglich, konnte jedoch unter Berücksichtigung ihrer bakteriellen Symbionten
erfolgen. Während Flagellaten der Gattung Metadevescovina einen dichten Besatz
von Spirochaeten auf ihrer Oberfläche zeigen, sind Devescovina spp.
vollständig von filamentösen Bakterien bedeckt, welche den Bacteroidales
zugeordnet werden. Molekularphylogenetische Analysen von Devescovina spp. von
verschiedenen Vertretern der Kalotermitidae und ihren bakteriellen Symbionten
ergaben zwei verschiedene Szenarien bezüglich des Erwerbs dieser Symbionten:
Eine vertikale Weitergabe und eine horizontale Weitergabe. Es konnte gezeigt
werden, dass die Ektosymbionten eine monophyletische Gruppe innerhalb der
Bacteroidales bilden („Candidatus Armantifilum devescovinae“).
Kongruenzanalysen der Stammbäume von Devescovina spp. und „Candidatus
Armantifilum devescovinae“ dokumentierten eine strikte Kospeziation der
Partner. Eine obligate Symbiose der beiden Partner, und somit eine vertikale
Weitergabe der Bakterien innerhalb ihrer Wirtsflagellaten, konnte demnach
belegt werden. Der Erwerb von Symbionten durch horizontale Weitergabe von
anderen Wirtsflagellaten wurde dagegen für die im Zytoplasma vorkommenden
‚Endomicrobia‘ dokumentiert. Hier waren die nächsten Verwandten der mit den
Devescovina spp. assoziierten ‚Endomicrobia‘ Endosymbionten von phylogenetisch
nicht verwandten Termitenflagellaten. In einer weiteren Studie dieser Arbeit
wurden die multiplen Symbionten des Flagellaten Joenia annectens aus der
Trockenholztermite Kalotermes flavicollis identifiziert und lokalisiert (full-
cycle-rRNA approach). Ultrastrukturelle Untersuchungen ermöglichten eine
morphologische Beschreibung der gefundenen Phylotypen. Basierend auf den
Assoziationen mit phylogenetisch verschiedenen Symbionten konnten zwei
Populationen von J. annectens unterschieden werden. Gestützt wurde das
Ergebnis durch die Analyse der SSU rRNA Gensequenzen von J. annectens (0,8%
Sequenzunterschied zwischen beiden Populationen). Beide
Flagellatenpopulationen waren jeweils mit eigenen Ektosymbionten des Phylums
Bacteroidetes assoziiert. Dahingegen beherbergte nur eine der beiden
Populationen von J. annectens einen Vertreter der ‚Endomicrobia‘ im
Zytoplasma. Das Fehlen von ‚Endomicrobia‘-Symbionten bei vielen Flagellaten
der gleichen Population zeigt ein weiteres Beispiel dafür, dass diese
Symbionten nicht immer mit ihren Wirtsflagellaten kospeziieren. Die Ergebnisse
meiner Arbeit haben wichtige Erkenntnisse zur Spezifität der Symbiosen
zwischen Termitenflagellaten und ihrer bakteriellen Symbionten gebracht. Sie
stellen somit eine Grundvoraussetzung für die anstehende Erforschung der
funktionellen Aspekte dieser Symbiosen dar. Eine Beteiligung der bakteriellen
Symbionten am Stickstoffstoffwechsel der Flagellaten wird diskutiert
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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