@phdthesis{Lind2016,
  author    = {Lind, Christof Martin},
  title     = {W{\"a}hrend der Evolution von Landpflanzen geriet der Anionenkanal SLAC1 unter die Kontrolle des ABA-Signalwegs},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-141669},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2016},
  abstract  = {Die ersten Landpflanzen standen vor der Herausforderung sich mit der wechselnden Verf{\"u}gbarkeit von Wasser an Land arrangieren zu m{\"u}ssen. Daraus ergab sich die Notwendigkeit den Wasserverlust zu minimieren und dennoch ausreichend CO2 f{\"u}r die Photosynthese aufzunehmen (Raven, 2002). Im Laufe der Evolution der Pflanzen entstanden mehrere Anpassungen an diese neuen Gegebenheiten, die schließlich auch zur Entstehung von regulierbaren {\"O}ffnungen, den Stomata, in der Blattepidermis f{\"u}hrte. Zwei Schließzellen umschließen das Stoma und regulieren {\"u}ber die Aufnahme oder Abgabe von osmotisch-aktiven Teilchen ihren Turgordruck und damit die {\"O}ffnungsweite des Stomas. Das Kation Kalium und die Anionen Chlorid und Nitrat repr{\"a}sentieren die Hauptosmotika, die je nach Bedarf durch Transportproteine {\"u}ber die Plasmamembran der Schließzellen geschleust werden. In den Samenpflanzen wie zum Beispiel der Modellpflanze Arabidopsis thaliana, ist der Signalweg in Schließzellen, der bei Trockenheit zu einem schnellen Schluss des Stomas f{\"u}hrt bereits sehr gut untersucht. Bei Wassermangel synthetisiert die Pflanze das Trockenstresshormon ABA (Abscisins{\"a}ure). Das Hormon wird durch ABA-Rezeptoren erkannt und resultiert schließlich in der Aktivit{\"a}t der Proteinkinase OST1. Daraufhin reguliert diese Kinase zum einen die Transkription ABA-abh{\"a}ngiger Gene, die der Pflanze eine langfristige Adaptation an Trockenheit und Austrocknungstoleranz verleiht. Zum anderen, phosphoryliert OST1 den Anionenkanal SLAC1 und aktiviert ihn so. Die Aktivit{\"a}t des Kanals initiiert schließlich den Stomaschluss durch einen Ausstrom von Anionen aus den Schließzellen, der mit einer Depolarisation der Schließzellmembran einhergeht. Der ABA-Signalweg, der zur transkriptionellen Regulation von Genen und der damit verbunden Trockentoleranz f{\"u}hrt ist ein sehr stark konservierter und evolutiv sehr alter Signalweg, der in allen Geweben von Pflanzen bei Trockenheit beschritten wird. Der schnelle ABA-Signalweg, der die Aktivit{\"a}t der SLAC1 Anionenkan{\"a}le reguliert, ist auf Schließzellen begrenzt. Da sich Schließzellen aber erst sp{\"a}t in der Evolution von Landpflanzen etablierten, erhob sich die Frage, wann in der Evolution geriet SLAC1 unter die Kontrolle das ABA-Signalwegs? Geht diese Regulation von SLAC1 mit der Entstehung von Schließzellen einher oder bestand dieser Regulationsmechanismus bereits in Pflanzen, die keine Schließzellen besitzen. Zur Beantwortung dieser Frage untersuchte ich die einzelnen Komponenten des Signalwegs und ihre Beziehungen zu einander im heterologen Expressionssystem der Xenopus laevis Oozyten. Im Laufe dieser Arbeit wurden Schl{\"u}sselelemente des ABA-Signalwegs aus sechs verschiedenen Versuchspflanzen kloniert und in Oozyten charakterisiert. F{\"u}r die Untersuchung der Evolution des schnellen ABA-Signalwegs wurden die sechs Versuchspflanzen aus je einem rezenten Vertreter der Gr{\"u}nalgen (Klebsormidium nitens), der Lebermoose (Marchantia polymorpha), der Laubmoose (Physcomitrella patens), der Lycophyten (Selaginella moellendorffii) und der Farne (Ceratopteris richardii) ausgew{\"a}hlt und mit der Samenpflanze Arabidopsis thaliana verglichen. Die sechs Pflanzengruppen spalteten sich an unterschiedlichen Zeitpunkten im Laufe der pflanzlichen Evolution von der Entwicklung der restlichen Pflanzen ab und erlauben so einen bestm{\"o}glichen Einblick in den jeweiligen Entwicklungsstand der Landpflanzen w{\"a}hrend der Entstehung der einzelnen Pflanzenfamilien. Obwohl sich die ersten Stomata erst in den Laubmoosen entwickelten, besitzen schon die Gr{\"u}nalgen OST1-Kinasen und SLAC1-Kan{\"a}le. Interessanterweise konnte wir zeigen, dass schon die fr{\"u}hen OST1-Kinasen aus Algen und Moosen dazu in der Lage sind, in den h{\"o}her entwickelten Samenpflanzen die Rolle in der Regulation der ABA-abh{\"a}ngigen Expression von Genen zu {\"u}bernehmen. Außerdem zeigte sich im Laufe meiner biophysikalischen Untersuchungen, dass alle dreizehn getesteten OST1-Kinasen aus den sechs unterschiedlichen Versuchspflanzenarten in Lage sind, den Anionenkanal SLAC1 aus Arabidopsis in Xenopus Oozyten zu aktivieren. Diese Austauschbarkeit von den AtSLAC1-aktivierenden Kinasen deutet auf eine sehr starke Konservierung der Struktur und Funktion von OST1 hin. Anders verhielt es sich bei der funktionellen Analyse der Anionenkan{\"a}le aus den verschiedenen Versuchspflanzen: Hier bildete nur der evolution{\"a}r gesehen j{\"u}ngsten SLAC-Kanal AtSLAC1 aus Arabidopsis ein funktionelles P{\"a}rchen mit OST1. Die SLAC1 Kan{\"a}le aus der Gr{\"u}nalge, dem Lebermoos, den Lycophyten und dem Farn blieben ohne messbare Aktivit{\"a}t bei einer Co-expression mit den verschiedenen OST1 Kinasen. Nur beim Laubmoos (Physcomitrella patens) konnte noch ein funktionelles Kinase-Anionenkanal P{\"a}rchen gefunden werden. Struktur-Funktionsuntersuchungen erlaubten mir schließlich zu zeigen, dass bestimmte funktionelle Dom{\"a}nen sowohl im N-terminus als auch im C-terminus von SLAC1 erforderlich sind, um eine Aktivierung des Kanals durch OST1 Kinasen sicherzustellen.},
  subject      = {Evolution},
  language  = {de}
}
@article{ArhondakisFrousiosIliopoulosetal.2011,
  author    = {Arhondakis, Stilianos and Frousios, Kimon and Iliopoulos, Costas S. and Pissis, Solon P. and Tischler, German and Kossida, Sophia},
  title     = {Transcriptome map of mouse isochores},
  series = {BMC Genomics},
  volume    = {12},
  journal   = {BMC Genomics},
  number    = {511},
  doi       = {10.1186/1471-2164-12-511},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-142773},
  pages     = {1-9},
  year      = {2011},
  abstract  = {Background: The availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression profiles for a variety of tissues, conditions, and species. In this study, using RNA-seq data for three distinct tissues (brain, liver, and muscle), we investigate how base composition affects mammalian gene expression, an issue of prime practical and evolutionary interest. Results: We present the transcriptome map of the mouse isochores (DNA segments with a fairly homogeneous base composition) for the three different tissues and the effects of isochores' base composition on their expression activity. Our analyses also cover the relations between the genes' expression activity and their localization in the isochore families. Conclusions: This study is the first where next-generation sequencing data are used to associate the effects of both genomic and genic compositional properties to their corresponding expression activity. Our findings confirm previous results, and further support the existence of a relationship between isochores and gene expression. This relationship corroborates that isochores are primarily a product of evolutionary adaptation rather than a simple by-product of neutral evolutionary processes.},
  language  = {en}
}
@phdthesis{Dornhaus2002,
  author    = {Dornhaus, Anna},
  title     = {The role of communication in the foraging process of social bees},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-3468},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2002},
  abstract  = {In the various groups of social bees, different systems of communication about food sources occur. These communication systems are different solutions to a common problem of social insects: efficiently allocating the necessary number of workers first to the task of foraging and second to the most profitable food sources. The solution chosen by each species depends on the particular ecological circumstances as well as the evolutionary history of that species. For example, the outstanding difference between the bumble bee and the honey bee system is that honey bees can communicate the location of profitable food sources to nestmates, which bumble bees cannot. To identify possible selection pressures that could explain this difference, I have quantified the benefits of communicating location in honey bees. I show that these strongly depend on the habitat, and that communicating location might not benefit bees in temperate habitats. This could be due to the differing spatial distributions of resources in different habitats, in particular between temperate and tropical regions. These distributions may be the reason why the mostly temperate-living bumble bees have never evolved a communication system that allows them to transfer information on location of food sources, whereas most tropical social bees (all honey bees and many stingless bees) are able to recruit nestmates to specific points in their foraging range. Nevertheless, I show that in bumble bees the allocation of workers to foraging is also regulated by communication. Successful foragers distribute in the nest a pheromone which alerts other bees to the presence of food. This pheromone stems from a tergite gland, the function of which had not been identified previously. Usage of a pheromone in the nest to alert other individuals to forage has not been described in other social insects, and might constitute a new mode of communicating about food sources. The signal might be modulated depending on the quality of the food source. Bees in the nest sample the nectar that has been brought into the nest. Their decision whether to go out and forage depends not only on the pheromone signal, but also on the quality of the nectar they have sampled. In this way, foraging activity of a bumble bee colony is adjusted to foraging conditions, which means most bees are allocated to foraging only if high-quality food sources are available. In addition, foraging activity is adjusted to the amount of food already stored. In a colony with full honeypots, no new bees are allocated to foraging. These results help us understand how the allocation of workers to the task of food collection is regulated according to external and internal nest conditions in bumble bees.},
  subject      = {Hummel},
  language  = {en}
}
@phdthesis{Pinkert2008,
  author    = {Pinkert, Stefan},
  title     = {The human proteome is shaped by evolution and interactions},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-35566},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2008},
  abstract  = {Das menschliche Genom ist seit 2001 komplett sequenziert. Ein Großteil der Proteine wurde mittlerweile beschrieben und t{\"a}glich werden bioinformatische Vorhersagen praktisch best{\"a}tigt. Als weiteres Großprojekt wurde k{\"u}rzlich die Sequenzierung des Genoms von 1000 Menschen gestartet. Trotzdem ist immer noch wenig {\"u}ber die Evolution des gesamten menschlichen Proteoms bekannt. Proteindom{\"a}nen und ihre Kombinationen sind teilweise sehr detailliert erforscht, aber es wurden noch nicht alle Dom{\"a}nenarchitekturen des Menschen in ihrer Gesamtheit miteinander verglichen. Der verwendete große hochqualitative Datensatz von Protein-Protein-Interaktionen und Komplexen stammt aus dem Jahr 2006 und erm{\"o}glicht es erstmals das menschliche Proteom mit einer vorher nicht m{\"o}glichen Genauigkeit analysieren zu k{\"o}nnen. Hochentwickelte Cluster Algorithmen und die Verf{\"u}gbarkeit von großer Rechenkapazit{\"a}t bef{\"a}higen uns neue Information {\"u}ber Proteinnetzwerke ohne weitere Laborarbeit zu gewinnen. Die vorliegende Arbeit analysiert das menschliche Proteom auf drei verschiedenen Ebenen. Zuerst wurde der Ursprung von Proteinen basierend auf ihrer Dom{\"a}nenarchitektur analysiert, danach wurden Protein-Protein-Interaktionen untersucht und schließlich erfolgte Einteilung der Proteine nach ihren vorhandenen und fehlenden Interaktionen. Die meisten bekannten Proteine enthalten mindestens eine Dom{\"a}ne und die Proteinfunktion ergibt sich aus der Summe der Funktionen der einzelnen enthaltenen Dom{\"a}nen. Proteine, die auf der gleichen Dom{\"a}nenarchitektur basieren, das heißt die die gleichen Dom{\"a}nen in derselben Reihenfolge besitzen, sind homolog und daher aus einem gemeinsamen urspr{\"u}nglichen Protein entstanden. Die Dom{\"a}nenarchitekturen der urspr{\"u}nglichen Proteine wurden f{\"u}r 750000 Proteine aus 1313 Spezies bestimmt. Die Gruppierung von Spezies und ihrer Proteine ergibt sich aus taxonomischen Daten von NCBI-Taxonomy, welche mit zus{\"a}tzlichen Informationen basierend auf molekularen Markern erg{\"a}nzt wurden. Der resultierende Datensatz, bestehend aus 5817 Dom{\"a}nen und 32868 Dom{\"a}nenarchitekturen, war die Grundlage f{\"u}r die Bestimmung des Ursprungs der Proteine aufgrund ihrer Dom{\"a}nenarchitekturen. Es wurde festgestellt, dass nur ein kleiner Teil der neu evolvierten Dom{\"a}nenarchitekturen eines Taxons gleichzeitig auch im selben Taxon neu entstandene Proteindom{\"a}nen enth{\"a}lt. Ein weiteres Ergebnis war, dass Dom{\"a}nenarchitekturen im Verlauf der Evolution l{\"a}nger und komplexer werden, und dass so verschiedene Organismen wie der Fadenwurm, die Fruchtfliege und der Mensch die gleiche Menge an unterschiedlichen Proteinen haben, aber deutliche Unterschiede in der Anzahl ihrer Dom{\"a}nenarchitekturen aufweisen. Der zweite Teil besch{\"a}ftigt sich mit der Frage wie neu entstandene Proteine Bindungen mit dem schon bestehenden Proteinnetzwerk eingehen. In fr{\"u}heren Arbeiten wurde gezeigt, dass das Protein-Interaktions-Netzwerk ein skalenfreies Netz ist. Skalenfreie Netze, wie zum Beispiel das Internet, bestehen aus wenigen Knoten mit vielen Interaktionen, genannt Hubs, und andererseits aus vielen Knoten mit wenigen Interaktionen. Man vermutet, dass zwei Mechanismen zur Entstehung solcher Netzwerke f{\"u}hren. Erstens m{\"u}ssen neue Proteine um auch Teil des Proteinnetzwerkes zu werden mit Proteinen interagieren, die bereits Teil des Netzwerkes sind. Zweitens interagieren die neuen Proteine, gem{\"a}ß der Theorie der bevorzugten Bindung, mit h{\"o}herer Wahrscheinlichkeit mit solchen Proteinen im Netzwerk, die schon an zahlreichen weiteren Protein-Interaktionen beteiligt sind. Die Human Protein Reference Database stellt ein auf Informationen aus in-vivo Experimenten beruhendes Proteinnetzwerk f{\"u}r menschliche Proteine zur Verf{\"u}gung. Basierend auf den in Kapitel I gewonnenen Informationen wurden die Proteine mit dem Ursprungstaxon ihrer Dom{\"a}nenarchitekturen versehen. Dadurch wurde gezeigt, dass ein Protein h{\"a}ufiger mit Proteinen, die im selben Taxon entstanden sind, interagiert, als mit Proteinen, die in anderen Taxa neu aufgetreten sind. Es stellte sich heraus, dass diese Interaktionsraten f{\"u}r alle Taxa deutlich h{\"o}her waren, als durch das Zufallsmodel vorhergesagt wurden. Alle Taxa enthalten den gleichen Anteil an Proteinen mit vielen Interaktionen. Diese zwei Ergebnisse sprechen dagegen, dass die bevorzugte Bindung der alleinige Mechanismus ist, der zum heutigen Aufbau des menschlichen Proteininteraktion-Netzwerks beigetragen hat. Im dritten Teil wurden Proteine basierend auf dem Vorhandensein und der Abwesenheit von Interaktionen in Gruppen eingeteilt. Proteinnetzwerke k{\"o}nnen in kleine hoch vernetzte Teile zerlegt werden, die eine spezifische Funktion aus{\"u}ben. Diese Gruppen k{\"o}nnen mit hoher statistischer Signifikanz berechnet werden, haben meistens jedoch keine biologische Relevanz. Mit einem neuen Algorithmus, welcher zus{\"a}tzlich zu Interaktionen auch Nicht-Interaktionen ber{\"u}cksichtigt, wurde ein Datensatz bestehend aus 8,756 Proteinen und 32,331 Interaktionen neu unterteilt. Eine Einteilung in elf Gruppen zeigte hohe auf Gene Ontology basierte Werte und die Gruppen konnten signifikant einzelnen Zellteilen zugeordnet werden. Eine Gruppe besteht aus Proteinen, welche wenige Interaktionen miteinander aber viele Interaktionen zu zwei benachbarten Gruppen besitzen. Diese Gruppe enth{\"a}lt eine signifikant erh{\"o}hte Anzahl an Transportproteinen und die zwei benachbarten Gruppen haben eine erh{\"o}hte Anzahl an einerseits extrazellul{\"a}ren und andererseits im Zytoplasma und an der Membran lokalisierten Proteinen. Der Algorithmus hat damit unter Beweis gestellt das die Ergebnisse nicht bloß statistisch sondern auch biologisch relevant sind. Wenn wir auch noch weit vom Verst{\"a}ndnis des Ursprungs der Spezies entfernt sind, so hat diese Arbeit doch einen Beitrag zum besseren Verst{\"a}ndnis der Evolution auf dem Level der Proteine geleistet. Im Speziellen wurden neue Erkenntnisse {\"u}ber die Beziehung von Proteindom{\"a}nen und Dom{\"a}nenarchitekturen, sowie ihre Pr{\"a}ferenzen f{\"u}r Interaktionspartner im Interaktionsnetzwerk gewonnen.},
  subject      = {Evolution},
  language  = {en}
}
@phdthesis{Fraune2014,
  author    = {Fraune, Johanna},
  title     = {The evolutionary history of the mammalian synaptonemal complex},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-100043},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2014},
  abstract  = {Der Synaptonemalkomplex (SC) ist eine hochkonservierte Proteinstruktur. Er weist eine dreiteili-ge, leiter{\"a}hnliche Organisation auf und ist f{\"u}r die stabile Paarung der homologen Chromosomen w{\"a}hrend der Prophase der ersten meiotischen Teilung verantwortlich, die auch als Synpase be-zeichnet wird. Fehler w{\"a}hrend der Synpase f{\"u}hren zu Aneuploidie oder Apoptose der sich entwi-ckelnden Keimzellen. Seit 1956 ist der SC Gegenstand intensiver Forschung. Seine Existenz wurde in zahlreichen Orga-nismen von der Hefe bis zum Menschen beschrieben. Seine Struktur aus zwei parallel verlaufen-den Lateralelementen (LE), die durch eine Vielzahl von sogenannten Transversalfilamenten (TF) verbunden werden und dem Zentralen Element (CE) in der Mitte des SC ist dabei offensichtlich {\"u}ber die Millionen von Jahren der Evolution erhalten geblieben. Einzelne Proteinkomponenten des SC wurden jedoch nur in wenigen Modelorganismen charakterisiert, darunter Saccharomyces cerevisiae, Arabidopsis thaliana, Drosophila melanogaster, Ceanorhabditis elegans und Mus mus-culus. Unerwarteter Weise gelang es bei dieser Charakterisierung nicht, eine evolution{\"a}re Ver-wandtschaft, d.h. eine Homologie zwischen den Proteinsequenzen der verschiedenen SCs nach-zuweisen. Diese Tatsache sprach gegen die grunds{\"a}tzliche Annahme, dass der SC in der Evolution nur einmal entstanden sei. Diese Arbeit hat sich nun der Aufgabe gewidmet, die Diskrepanz zwischen der hochkonservierten Struktur des SC und seiner augenscheinlich nicht-homologen Proteinzusammensetzung zu l{\"o}sen. Dabei beschr{\"a}nkt sie sich auf die Analyse des Tierreichs. Es ist die erste Studie zur Evolution des SC in Metazoa und demonstriert die Monophylie der S{\"a}uger SC Proteinkomponenten im Tierreich. Die Arbeit zeigt, dass mindestens vier von sieben SC Proteinen der Maus sp{\"a}testens im letzten gemeinsamen Vorfahren der Gewebetiere (Eumetazoa) enstanden sind und auch damals Teil ei-nes urspr{\"u}nglichen SC waren, wie er heute in dem Nesseltier Hydra zu finden ist. Dieser SC weist die typische Struktur auf und besitzt bereits alle notwendigen Komponenten, um die drei Dom{\"a}-nen - LE, TF und CE - zu assemblieren. Dar{\"u}ber hinaus ergaben die einzelnen Phylogenien der verschiedenen SC Proteine der Maus, dass der SC eine sehr dynamische Evolutionsgeschichte durchlaufen hat. Zus{\"a}tzliche Proteine wurden w{\"a}hrend der Entstehung der Bilateria und der Wir-beltiere in den SC integriert, w{\"a}hrend andere urspr{\"u}ngliche Komponenten m{\"o}glicherweise Gen-Duplikationen erfuhren bzw. besonders in der Linie der H{\"a}utungstiere verloren gingen oder sich stark ver{\"a}nderten. Es wird die These aufgestellt, dass die auf den ersten Blick nicht-homologen SC Proteine der Fruchtfliege und des Fadenwurms tats{\"a}chlich doch von den urspr{\"u}nglichen Prote-inenkomponenten abstammen, sich aber aufgrund der rasanten Evolution der Arthropoden und der Nematoden bis zu deren Unkenntlichkeit diversifizierten. Zus{\"a}tzlich stellt die Arbeit Hydra als alternatives wirbelloses Modellsystem f{\"u}r die Meiose- und SC-Forschung zu den {\"u}blichen Modellen D. melanogaster und C. elegans vor. Die k{\"u}rzlich gewon-nenen Erkenntnisse {\"u}ber den Hydra SC sowie der Einsatz der Standard-Methoden in diesem Orga-nismus werden in dem abschließenden Kapitel zusammengefasst und diskutiert.},
  subject      = {Synaptinemal-Komplex},
  language  = {en}
}
@phdthesis{Mitesser2006,
  author    = {Mitesser, Oliver},
  title     = {The evolution of insect life history strategies in a social context},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-22576},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2006},
  abstract  = {This thesis extends the classical theoretical work of Macevicz and Oster (1976, expanded by Oster and Wilson, 1978) on adaptive life history strategies in social insects. It focuses on the evolution of dynamic behavioural patterns (reproduction and activity) as a consequence of optimal allocation of energy and time resources. Mathematical modelling is based on detailed empirical observations in the model species Lasioglossum malachurum (Halictidae; Hymenoptera). The main topics are field observations, optimisation models for eusocial life histories, temporal variation in life history decisions, and annual colony cycles of eusocial insects.},
  subject      = {Schmalbienen},
  language  = {en}
}
@phdthesis{Koetschan2012,
  author    = {Koetschan, Christian},
  title     = {The Eukaryotic ITS2 Database - A workbench for modelling RNA sequence-structure evolution},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-73128},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2012},
  abstract  = {In den vergangenen Jahren etablierte sich der Marker „internal transcribed spacer 2" (ITS2) zu einem h{\"a}ufig genutzten Werkzeug in der molekularen Phylogenetik der Eukaryoten. Seine schnell evolvierende Sequenz eignet sich bestens f{\"u}r den Einsatz in niedrigeren phylogenetischen Ebenen. Die ITS2 faltet jedoch auch in eine sehr konservierte Sekund{\"a}rstruktur. Diese erm{\"o}glicht die Unterscheidung weit entfernter Arten. Eine Kombination aus beiden in einer Sequenzstrukturanalyse verbessert die Aufl{\"o}sung des Markers und erm{\"o}glicht die Rekonstruktion von robusteren B{\"a}umen auf h{\"o}herer taxonomischer Breite. Jedoch war die Durchf{\"u}hrung solch einer Analyse, die die Nutzung unterschiedlichster Programme und Datenbanken vorraussetzte, f{\"u}r den klassischen Biologen nicht einfach durchf{\"u}hrbar. Um diese H{\"u}rde zu umgehen, habe ich den „ITS2 Workbench" entwickelt, eine im Internet nutzbare Arbeitsplattform zur automatisierten sequenzstrukturbasierten phylogenetischen Analyse basierend auf der ITS2 (http://its2.bioapps.biozentrum.uni-wuerzburg.de). Die Entwicklung begann mit der L{\"a}ngenoptimierung unterschiedlicher „Hidden Markov Model" (HMM)-Topologien, die erfolgreich auf ein Modell zur Sequenzstrukturvorhersage der ITS2 angewandt wurden. Hierbei wird durch die Analyse von Sequenzbestandteilen in Kombination mit der L{\"a}ngenverteilung verschiedener Helixregionen die Struktur vorhergesagt. Anschließend konnte ich HMMs auch bei der Sequenzstrukturgenerierung einsetzen um die ITS2 innerhalb einer gegebenen Sequenz zu lokalisieren. Dieses neu implementierte Verfahren verdoppelte die Anzahl vorhergesagter Strukturen und verk{\"u}rzte die Laufzeit auf wenige Tage. Zusammen mit weiteren Optimierungen des Homologiemodellierungsprozesses kann ich nun ersch{\"o}pfend Sekund{\"a}rstrukturen in mehreren Interationen vorhersagen. Diese Optimierungen liefern derzeit 380.000 annotierte Sequenzen einschließlich 288.000 Strukturvorhersagen. Um diese Strukturen f{\"u}r die Berechnung von Alignments und phylogenetischen B{\"a}umen zu verwenden hab ich das R-Paket „treeforge" entwickelt. Es erm{\"o}glicht die Generierung von Sequenzstrukturalignments auf bis zu vier unterschiedlich kodierten Alphabeten. Damit k{\"o}nnen erstmals auch strukturelle Basenpaarungen in die Alignmentberechnung mit einbezogen werden, die eine Sch{\"a}tzung neuer Scorematrizen vorraussetzten. Das R-Paket erm{\"o}glicht zus{\"a}tzlich die Rekonstruktion von „Maximum Parsimony", „Maximum Likelihood" und „Neighbour Joining" B{\"a}umen auf allen vier Alphabeten mittels weniger Zeilen Programmcode. Das Paket wurde eingesetzt, um die noch umstrittene Phylogenie der „chlorophyceae" zu rekonstruieren und k{\"o}nnte in zuk{\"u}nftigen Versionen des ITS2 workbench verwendet werden. Die ITS2 Plattform basiert auf einer modernen und sehr umfangreichen Web 2.0 Oberfl{\"a}che und beinhaltet neuste AJAX und Web-Service Technologien. Sie umfasst die HMM basierte Sequenzannotation, Strukturvorhersage durch Energieminimierung bzw. Homologiemodellierung, Alignmentberechnung und Baumrekonstruktion basierend auf einem flexiblen Datenpool, der {\"A}nderungen am Datensatz automatisch aktualisiert. Zus{\"a}tzlich wird eine Detektion von Sequenzmotiven erm{\"o}glicht, die zur Kontrolle von Annotation und Strukturvorhersage dienen kann. Eine BLAST basierte Suche auf Sequenz- und Strukturebene bietet zus{\"a}tzlich eine Vereinfachung des Taxonsamplings. Alle Funktionen sowie die Nutzung der ITS2 Webseite sind in einer kurzen Videoanleitung dargestellt. Die Plattform l{\"a}sst jedoch nur eine bestimmte Gr{\"o}ße von Datens{\"a}tzen zu. Dies liegt vor allem an der erheblichen Rechenleistung, die bei diesen Berechnungen ben{\"o}tigt wird. Um die Funktion dieses Verfahrens auch auf großen Datenmengen zu demonstrieren, wurde eine voll automatisierte Rekonstruktion des Gr{\"u}nalgenbaumes (Chlorophyta) durchgef{\"u}hrt. Diese erfolgreiche, auf dem ITS2 Marker basierende Studie spricht f{\"u}r die Sequenz-Strukturanalyse auf weiteren Daten in der Phylogenetik. Hier bietet der ITS2 Workbench den idealen Ausgangspunkt.},
  subject      = {Ribosomale RNA},
  language  = {en}
}
@phdthesis{Drescher2011,
  author    = {Drescher, Jochen},
  title     = {The Ecology and Population structure of the invasive Yelllow Crazy Ant Anoplolepis gracilipes},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-57332},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2011},
  abstract  = {The invasive Yellow Crazy Ant Anoplolepis gracilipes is a widespread tropical ant species which is particularly common in anthropogenically disturbed habitats in South-East Asia and the Indopacific region. Its native range is unknown, and there is little information concerning its social structure as a potential mechanism facilitating invasion as well as its ecology in one of the putative native ranges, South-East Asia. Using mitochondrial DNA sequences, I demonstrated that the majority of the current Indopacific colonies were likely introduced from South-East Asian populations, which in turn may have been introduced much earlier from a yet unidentified native range. By conducting behavioral, genetic and chemical analyses, I found that A. gracilipes supercolonies contain closely related individuals, thus resembling enlarged versions of monogynous, polydomous colonies of other ant species. Furthermore, mutually aggressive A. gracilipes supercolonies were highly differentiated both genetically and chemically, suggesting limited or even absent gene flow between supercolonies. Intranidal mating and colony-budding are most likely the predominant, if not the exclusive mode of reproduction and dispersal strategy of A. gracilipes. Consequently, a positive feedback between genetic, chemical and behavioral traits may further enhance supercolony differentiation though genetic drift and neutral evolution. This potential scenario led to the hypothesis that absent gene flow between different A. gracilipes supercolonies may drive them towards different evolutionary pathways, possibly including speciation. Thus, I examined one potential way by which gene flow between supercolonies of an ant species without nuptial flights may be maintained, i.e. the immigration of sexuals into foreign supercolonies. The results suggest that this option of maintaining gene flow between different supercolonies is likely impaired by severe aggression of workers towards allocolonial sexuals. Moreover, breeding experiments involving males and queens from different supercolonies suggest that A. gracilipes supercolonies may already be on the verge of reproductive isolation, which might lead to the diversification of A. gracilipes into different species. Regarding the ecological consequences of its potential introduction to NE-Borneo, I could show that A. gracilipes supercolonies may affect the local ant fauna. The ant community within supercolonies was less diverse and differed in species composition from areas outside supercolonies. My data suggest that the ecological dominance of A. gracilipes within local ant communities was facilitated by monopolization of food sources within its supercolony territory, achieved by a combination of rapid recruitment, numerical dominance and pronounced interspecific aggression. A. gracilipes' distribution is almost exclusively limited to anthropogenically altered habitat, such as residential and agricultural areas. The rate at which habitat conversion takes place in NE-Borneo will provide A. gracilipes with a rapidly increasing abundance of suitable habitats, thus potentially entailing significant population growth. An potentially increasing population size and ecological dominance, however, are not features that are limited to invasive alien species, but may also occur in native species that become 'pests' in an increasing abundance of anthropogenically altered habitat. Lastly, I detected several ant guests in supercolonies of A. gracilipes. I subsequently describe the relationship between one of them (the cricket Myrmecophilus pallidithorax) and its ant host. By conducting behavioral bioassays and analyses of cuticular hydrocarbon (CHC) profiles, I revealed that although M. pallidithorax is attacked and consumed by A. gracilipes whenever possible, it may evade aggression from its host by a combination of supreme agility and, possibly, chemical deception. This thesis adds to our general understanding of biological invasions by contributing species-specific data on a previously understudied invasive organism, the Yellow Crazy Ant Anoplolepis gracilipes. Introductions which may have occurred a long time ago may make it difficult to determine whether a given species is an introduced invader or a native pest species, as both may have pronounced ecological effects in native species communities. Furthermore, this thesis suggests that supercolonialism in invasive ants may not be an evolutionary dead end, but that it may possibly give rise to new species due to reproductive boundaries between supercolonies evoked by peculiar mating and dispersal strategies.},
  subject      = {Dem{\"o}kologie},
  language  = {en}
}
@phdthesis{Winkel2009,
  author    = {Winkel, Karoline},
  title     = {Synaptonemalkomplexprotein SYCP1: Bindungspartner, Polymerisationseigenschaften und evolution{\"a}re Aspekte},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-43955},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2009},
  abstract  = {Synaptonemal Komplexe (SC) sind evolution{\"a}r konservierte, meiosespezifische, protein{\"o}se Strukturen, die maßgeblich an Synapsis, Rekombination und Segregation der homologen Chromosomen beteiligt sind. Sie zeigen eine dreigliedrige strickleiter-artige Organisation, die sich aus i) zwei Lateralelementen (LE), an die das Chromatin der Homologen angelagert ist, ii) zahlreichen Transversalfilamenten (TF), welche die LE in einer reißverschlussartigen Weise miteinander verkn{\"u}pfen, und iii) einem zentralen Element (CE) zusammensetzt. Die Hauptproteinkomponenten der S{\"a}uger-SC sind das Transversalfilamentprotein SYCP1 und die Lateralelementproteine SYCP2 und SYCP3. Wie sich die SC-Struktur zusammenf{\"u}gt war bisher nur wenig verstanden; es war nicht bekannt wie die TF innerhalb der LE-Strukturen verankert sind und dabei die homologen Chromosomen verkn{\"u}pfen. Aufgrund dessen wurde die Interaktion zwischen den Proteinen SYCP1 und SYCP2 untersucht. Mit der Hilfe verschiedenster Interaktionssysteme konnte gezeigt werden, dass der C-Terminus von SYCP1 mit SYCP2 interagieren kann. Aufgrund der Bindungsf{\"a}higkeit zu beiden Proteinen, SYCP1 und SYCP3, kann angenommen werden, dass SYCP2 als Linker zwischen diesen Proteinen fungiert und somit m{\"o}glicherweise das fehlende Bindungsglied zwischen den Lateralelementen und Transversalfilamenten darstellt. Obwohl die SC-Struktur in der Evolution hochkonserviert ist, schien dies nicht f{\"u}r seine Protein-Untereinheiten zuzutreffen. Um die Struktur und Funktion des SC besser verstehen zu k{\"o}nnen, wurde ein Vergleich zwischen den orthologen SYCP1 Proteinen der evolution{\"a}r entfernten Spezies Ratte und Medaka erstellt. Abgesehen von den erheblichen Sequenzunterschieden die sich in 450 Millionen Jahren der Evolution angeh{\"a}uft haben, traten zwei bisher nicht identifizierte Sequenzmotive hervor, CM1 und CM2, die hochgradig konserviert sind. Anhand dieser Motive konnte in Datenbankanalysen erstmals ein Protein in Hydra vulgaris nachgewiesen werden, bei dem es sich um das orthologe Protein von SYCP1 handeln k{\"o}nnte. Im Vergleich mit dem SYCP1 der Ratte zeigten die Proteine aus Medaka und Hydra, neben den hoch konservierten CM1 und CM2, vergleichbare Dom{\"a}nenorganisationen und im heterologen System zudem sehr {\"a}hnliche Polymerisationseigenschaften. Diese Ergebnisse sprechen f{\"u}r eine evolution{\"a}re Konservierung von SYCP1.},
  subject      = {Meiose},
  language  = {de}
}
@unpublished{Dandekar2007,
  author    = {Dandekar, Thomas},
  title     = {Some general system properties of a living observer and the environment he explores},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-33537},
  year      = {2007},
  abstract  = {In a nice assay published in Nature in 1993 the physicist Richard God III started from a human observer and made a number of witty conclusions about our future prospects giving estimates for the existence of the Berlin Wall, the human race and all the rest of the universe. In the same spirit, we derive implications for "the meaning of life, the universe and all the rest" from few principles. Adams´ absurd answer "42" tells the lesson "garbage in / garbage out" - or suggests that the question is non calculable. We show that experience of "meaning" and to decide fundamental questions which can not be decided by formal systems imply central properties of life: Ever higher levels of internal representation of the world and an escalating tendency to become more complex. An observer, "collecting observations" and three measures for complexity are examined. A theory on living systems is derived focussing on their internal representation of information. Living systems are more complex than Kolmogorov complexity ("life is NOT simple") and overcome decision limits (G{\"o}del theorem) for formal systems as illustrated for cell cycle. Only a world with very fine tuned environments allows life. Such a world is itself rather complex and hence excessive large in its space of different states - a living observer has thus a high probability to reside in a complex and fine tuned universe.},
  subject      = {Komplex <Algebra>},
  language  = {en}
}
@phdthesis{Streinzer2013,
  author    = {Streinzer, Martin},
  title     = {Sexual dimorphism of the sensory systems in bees (Hymenoptera, Apoidea) and the evolution of sex-specific adaptations in the context of mating behavior},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-78689},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2013},
  abstract  = {Bees have had an intimate relationship with humans for millennia, as pollinators of fruit, vegetable and other crops and suppliers of honey, wax and other products. This relationship has led to an extensive understanding of their ecology and behavior. One of the most comprehensively understood species is the Western honeybee, Apis mellifera. Our understanding of sex-specific investment in other bees, however, has remained superficial. Signals and cues employed in bee foraging and mating behavior are reasonably well understood in only a handful of species and functional adaptations are described in some species. I explored the variety of sensory adaptations in three model systems within the bees. Females share a similar ecology and similar functional morphologies are to be expected. Males, engage mainly in mating behavior. A variety of male mating strategies has been described which differ in their spatiotemporal features and in the signals and cues involved, and thus selection pressures. As a consequence, males' sensory systems are more diverse than those of females. In the first part I studied adaptations of the visual system in honeybees. I compared sex and caste-specific eye morphology among 5 species (Apis andreniformis, A. cerana, A. dorsata, A. florea, A. mellifera). I found a strong correlation between body size and eye size in both female castes. Queens have a relatively reduced visual system which is in line with the reduced role of visual perception in their life history. Workers differed in eye size and functional morphology, which corresponds to known foraging differences among species. In males, the eyes are conspicuously enlarged in all species, but a disproportionate enlargement was found in two species (A. dorsata, A. florea). I further demonstrate a correlation between male visual parameters and mating flight time, and propose that light intensities play an important role in the species-specific timing of mating flights. In the second study I investigated eye morphology differences among two phenotypes of drones in the Western honeybee. Besides normal-sized drones, smaller drones are reared in the colony, and suffer from reduced reproductive success. My results suggest that the smaller phenotype does not differ in spatial resolution of its visual system, but suffers from reduced light and contrast sensitivity which may exacerbate the reduction in reproductive success caused by other factors. In the third study I investigated the morphology of the visual system in bumblebees. I explored the association between male eye size and mating behavior and investigated the diversity of compound eye morphology among workers, queens and males in 11 species. I identified adaptations of workers that correlate with distinct foraging differences among species. Bumblebee queens must, in contrast to honeybees, fulfill similar tasks as workers in the first part of their life, and correspondingly visual parameters are similar among both female castes. Enlarged male eyes are found in several subgenera and have evolved several times independently within the genus, which I demonstrate using phylogenetic informed statistics. Males of these species engage in visually guided mating behavior. I find similarities in the functional eye morphology among large-eyed males in four subgenera, suggesting convergent evolution as adaptation to similar visual tasks. In the remaining species, males do not differ significantly from workers in their eye morphology. In the fourth study I investigated the sexual dimorphism of the visual system in a solitary bee species. Males of Eucera berlandi patrol nesting sites and compete for first access to virgin females. Males have enlarged eyes and better spatial resolution in their frontal eye region. In a behavioral study, I tested the effect of target size and speed on male mate catching success. 3-D reconstructions of the chasing flights revealed that angular target size is an important parameter in male chasing behavior. I discuss similarities to other insects that face similar problems in visual target detection. In the fifth study I examined the olfactory system of E. berlandi. Males have extremely long antennae. To investigate the anatomical grounds of this elongation I studied antennal morphology in detail in the periphery and follow the sexual dimorphism into the brain. Functional adaptations were found in males (e.g. longer antennae, a multiplication of olfactory sensilla and receptor neurons, hypertrophied macroglomeruli, a numerical reduction of glomeruli in males and sexually dimorphic investment in higher order processing regions in the brain), which were similar to those observed in honeybee drones. The similarities and differences are discussed in the context of solitary vs. eusocial lifestyle and the corresponding consequences for selection acting on males.},
  subject      = {Biene},
  language  = {en}
}
@phdthesis{Keller2010,
  author    = {Keller, Alexander},
  title     = {Secondary (and tertiary) structure of the ITS2 and its application for phylogenetic tree reconstructions and species identification},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-56151},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {Biodiversity may be investigated and explored by the means of genetic sequence information and molecular phylogenetics. Yet, with ribosomal genes, information for phylogenetic studies may not only be retained from the primary sequence, but also from the secondary structure. Software that is able to cope with two dimensional data and designed to answer taxonomic questions has been recently developed and published as a new scientific pipeline. This thesis is concerned with expanding this pipeline by a tool that facialiates the annotation of a ribosomal region, namely the ITS2. We were also able to show that this states a crucial step for secondary structure phylogenetics and for data allocation of the ITS2-database. This resulting freely available tool determines high quality annotations. In a further study, the complete phylogenetic pipeline has been evaluated on a theoretical basis in a comprehensive simulation study. We were able to show that both, the accuracy and the robustness of phylogenetic trees are largely improved by the approach. The second major part of this thesis concentrates on case studies that applied this pipeline to resolve questions in taxonomy and ecology. We were able to determine several independent phylogenies within the green algae that further corroborate the idea that secondary structures improve the obtainable phylogenetic signal, but now from a biological perspective. This approach was applicable in studies on the species and genus level, but due to the conservation of the secondary structure also for investigations on the deeper level of taxonomy. An additional case study with blue butterflies indicates that this approach is not restricted to plants, but may also be used for metazoan phylogenies. The importance of high quality phylogenetic trees is indicated by two ecological studies that have been conducted. By integrating secondary structure phylogenetics, we were able to answer questions about the evolution of ant-plant interactions and of communities of bacteria residing on different plant tissues. Finally, we speculate how phylogenetic methods with RNA may be further enhanced by integration of the third dimension. This has been a speculative idea that was supplemented with a small phylogenetic example, however it shows that the great potential of structural phylogenetics has not been fully exploited yet. Altogether, this thesis comprises aspects of several different biological disciplines, which are evolutionary biology and biodiversity research, community and invasion ecology as well as molecular and structural biology. Further, it is complemented by statistical approaches and development of informatical software. All these different research areas are combined by the means of bioinformatics as the central connective link into one comprehensive thesis.},
  subject      = {Phylogenie},
  language  = {en}
}
@phdthesis{Schilder1999,
  author    = {Schilder, Klaus},
  title     = {Safer without Sex?},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-1977},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {1999},
  abstract  = {Highly eusocial insect societies, such as all known ants, are typically characterized by a reproductive division of labor between queens, who are inseminated and reproduce, and virgin workers, who engage in foraging, nest maintenance and brood care. In most species workers have little reproductive options left: They usually produce haploid males by arrhenotokous parthenogenesis, both in the queenright and queenless condition. In the phylogenetically primitive subfamily Ponerinae reproductive caste dimorphism is much less pronounced: Ovarian morphology is rather similar in queens and workers, which additionally retain a spermatheca. In many ponerine species workers mate and may have completely replaced the queen caste. This similarity in reproductive potential provides for the evolution of diverse reproductive systems. In addition, it increases the opportunity for reproductive conflicts among nestmates substantially. Only in a handful of ant species, including Platythyrea punctata, workers are also able to rear diploid female offspring from unfertilized eggs by thelytokous parthenogenesis. The small ponerine ant P. punctata (Smith) is the only New World member of the genus reaching as far north as the southern USA, with its center of distribution in Central America and the West Indies. P. punctata occurs in a range of forest habitats including subtropical hardwood forests as well as tropical rain forests. In addition to queens, gamergates and thelytokous workers co-occur in the same species. This remarkable complexity of reproductive strategies makes P. punctata unique within ants and provides an ideal model system for the investigation of reproductive conflicts within the female caste. Colonies are usually found in rotten branches on the forest floor but may also be present in higher strata. Colonies contained on average 60 workers, with a maximum colony size of 148 workers. Queens were present in only ten percent of the colonies collected from Florida, but completely absent both from the populations studied in Barbados and Puerto Rico. Males were generally rare. In addition, morphological intermediates between workers and queens (so-called intercastes) were found in 16 colonies collected in Florida. Their thorax morphology varied from an almost worker-like to an almost queen-like thorax structure. Queen and intercaste size, however, did not differ from those of workers. Although workers taken from colonies directly after collection from the field engaged in aggressive interactions, nestmate discrimination ceased in the laboratory suggesting that recognition cues used are derived from the environment. Only one of six queens dissected was found to be inseminated but not fertile. Instead, in most queenless colonies, a single uninseminated worker monopolized reproduction by means of thelytokous parthenogenesis. A single mated, reproductive worker (gamergate) was found dominating reproduction in the presence of an inseminated alate queen only in one of the Florida colonies. The regulation of reproduction was closely examined in ten experimental groups of virgin laboratory-reared workers, in which one worker typically dominated reproduction by thelytoky despite the presence of several individuals with elongated, developing ovaries. In each group only one worker was observed to oviposit. Conflict over reproduction was intense consisting of ritualized physical aggression between some nestmates including antennal boxing, biting, dragging, leap and immobilization behaviors. The average frequency of interactions was low. Aggressive interactions allowed to construct non-linear matrices of social rank. On average, only five workers were responsible for 90 percent of total agonistic interactions. In 80 percent of the groups the rate of agonistic interactions increased after the experimental removal of the reproductive worker. While antennal boxing and biting were the most frequent forms of agonistic behaviors both before and after the removal, biting and dragging increased significantly after the removal indicating that agonistic interactions increased in intensity. Once a worker obtains a high social status it is maintained without the need for physical aggression. The replacement of reproductives by another worker did however not closely correlate with the new reproductive's prior social status. Age, however, had a profound influence on the individual rate of agonistic interactions that workers initiated. Especially younger adults (up to two month of age) and callows were responsible for the increase in observed aggression after the supersedure of the old reproductive. These individuals have a higher chance to become reproductive since older, foraging workers may not be able to develop their ovaries. Aggressions among older workers ceased with increasing age. Workers that already started to develop their ovaries should pose the greatest threat to any reproductive individual. Indeed, dissection of all experimental group revealed that aggression was significantly more often directed towards both individuals with undeveloped and developing ovaries as compared to workers that had degenerated ovaries. In all experimental groups reproductive dominance was achieved by callows or younger workers not older than four month. Age is a better predictor of reproductive dominance than social status as inferred from physical interactions. Since no overt conflict between genetical identical individuals is expected, in P. punctata the function of agonistic interactions in all-worker colonies, given the predominance of thelytokous parthenogenesis, remains unclear. Physical aggression could alternatively function to facilitate a smooth division of non-reproductive labor thereby increasing overall colony efficiency. Asexuality is often thought to constitute an evolutionary dead end as compared with sexual reproduction because genetic recombination is limited or nonexistent in parthenogenetic populations. Microsatellite markers were developed to investigate the consequences of thelytokous reproduction on the genetic structure of four natural populations of P. punctata. In the analysis of 314 workers taken from 51 colonies, low intraspecific levels of variation at all loci, expressed both as the number of alleles detected and heterozygosities observed, was detected. Surprisingly, there was almost no differentiation within populations. Populations rather had a clonal structure, with all individuals from all colonies usually sharing the same genotype. This low level of genotypic diversity reflects the predominance of thelytoky under natural conditions in four populations of P. punctata. In addition, the specificity of ten dinucleotide microsatellite loci developed for P. punctata was investigated in 29 ant species comprising four different subfamilies by cross-species amplification. Positive amplification was only obtained in a limited number of species indicating that sequences flanking the hypervariable region are often not sufficiently conserved to allow amplification, even within the same genus. The karyotype of P. punctata (2n = 84) is one of the highest chromosome numbers reported in ants so far. A first investigation did not show any indication of polyploidy, a phenomenon which has been reported to be associated with the occurrence of parthenogenesis. Thelytokous parthenogenesis does not appear to be a very common phenomenon in the Hymenoptera. It is patchily distributed and restricted to taxa at the distant tips of phylogenies. Within the Formicidae, thelytoky has been demonstrated only in four phylogenetically very distant species, including P. punctata. Despite its advantages, severe costs and constraints may have restricted its rapid evolution and persistence over time. The mechanisms of thelytokous parthenogenesis and its ecological correlates are reviewed for the known cases in the Hymenoptera. Investigating the occurrence of sexual reproduction in asexual lineages indicates that thelytokous parthenogenesis may not be irreversible. In P. punctata the occasional production of sexuals in some of the colonies may provide opportunity for outbreeding and genetic recombination. Thelytoky can thus function as a conditional reproductive strategy. Thelytoky in P. punctata possibly evolved as an adaptation to the risk of colony orphanage or the foundation of new colonies by fission. The current adaptive value of physical aggression and the production of sexuals in clonal populations, where relatedness asymmetries are virtually absent, however is less clear. Quite contrary, thelytoky could thereby serve as the stepping stone for the subsequent loss of the queen caste in P. punctata. Although P. punctata clearly fulfills all three conditions of eusociality, the evolution of thelytoky is interpreted as a first step in a secondary reverse social evolution towards a social system more primitive than eusociality.},
  subject      = {Ameisenstaat},
  language  = {en}
}
@phdthesis{Kubisch2012,
  author    = {Kubisch, Alexander},
  title     = {Range border formation in the light of dispersal evolution},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-70639},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2012},
  abstract  = {Understanding the emergence of species' ranges is one of the most fundamental challenges in ecology. Early on, geographical barriers were identified as obvious natural constraints to the spread of species. However, many range borders occur along gradually changing landscapes, where no sharp barriers are obvious. Mechanistic explanations for this seeming contradiction incorporate environmental gradients that either affect the spatio-temporal variability of conditions or the increasing fragmentation of habitat. Additionally, biological mechanisms like Allee effects (i.e. decreased growth rates at low population sizes or densities), condition-dependent dispersal, and biological interactions with other species have been shown to severely affect the location of range margins. The role of dispersal has been in the focus of many studies dealing with range border formation. Dispersal is known to be highly plastic and evolvable, even over short ecological time-scales. However, only few studies concentrated on the impact of evolving dispersal on range dynamics. This thesis aims at filling this gap. I study the influence of evolving dispersal rates on the persistence of spatially structured populations in environmental gradients and its consequences for the establishment of range borders. More specially I investigate scenarios of range formation in equilibrium, periods of range expansion, and range shifts under global climate change ...},
  subject      = {Areal},
  language  = {en}
}
@phdthesis{Rueppell2000,
  author    = {R{\"u}ppell, Olav},
  title     = {Queen size dimorphism in ants},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-1914},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2000},
  abstract  = {Many polymorphisms are linked to alternative reproductive strategies. In animals, this is particularly common in males. Ant queens are an important exception. The case of ant queen size dimorphisms has not been studied in sufficient detail, and thus this thesis aimed at elucidating causes and consequences of the different size of small (microgynous) and large (macrogynous)ant queens using the North American ant species Leptothorax rugatulus as a model system. Employing neutral genetic markers, no evidence for a taxonomically relevant separation of the gene pools of macrogynes and microgynes was found. Queens in polygynous colonies were highly related to each other, supporting the hypothesis that colonies with more than one queen commonly arise by secondary polygyny, i.e. by the adoption of daughter queens into their natal colonies. These results and conclusions are also true for the newly discovered queen size polymorphism in Leptothorax cf. andrei. Several lines of evidence favor the view that macrogynes predominantly found their colonies independently, while microgynes are specialized for dependent colony founding by readoption. Under natural conditions, mother and daughter size are highly correlated and this is also true for laboratory colonies. However, the size of developing queens is influenced by queens present in the colony. Comparing populations across the distribution range, it turns out that queen morphology (head width and ovariole number) is more differentiated among populations than worker morphology (coloration, multivariate size and shape), colony characteristics (queen and worker number per colony) or neutral genetic variation. Northern and southern populations differed consistently which indicates the possibility of two different species. The queen size dimorphism in L. rugatulus did neither influence the sex ratio produced by a colony, nor its ratio of workers to gynes. However, the sex ratio covaried strongly across populations with the average number of queens per colony in accordance with sex ratio theory. At the colony level, sex ratio could not be explained by current theory and a hypothesis at the colony-level was suggested. Furthermore, queen body size has no significant influence on the amount of reproductive skew among queens. Generally, the skew in L. rugatulus is low, and supports incomplete control models, rather than the classic skew models. In eight of fourteen mixed or microgynous colonies, the relative contributions of individual queens to workers, gynes and males were significantly different. This was mainly due to the fact that relative body size was negatively correlated with the ratio of gynes to workers produced. This supports the kin conflict over caste determination hypothesis which views microgyny as a selfish reproductive tactic.},
  subject      = {Ameisen},
  language  = {en}
}
@phdthesis{Vershenya2010,
  author    = {Vershenya, Stanislav},
  title     = {Quantitative and qualitative analyses of in-paralogs},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-51358},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {In our analysis I was interested in the gene duplications, with focus on in-paralogs. In-paralogs are gene duplicates which arose after species split. Here I analysed the in-paralogs quantitatively, as well as qualitatively. For quantitative analysis genomes of 21 species were taken. Most of them have vastly different lifestyles with maximum evolutionary distance between them 1100 million years. Species included mammals, fish, insects and worm, plus some other chordates. All the species were pairwised analysed by the Inparanoid software, and in-paralogs matrix were built representing number of in-paralogs in all vs. all manner. Based on the in-paralogs matrix I tried to reconstruct the evolutionary tree using in-paralog numbers as evolutionary distance. If all 21 species were used the resulting tree was very far from real one: a lot of species were misplaced. However if the number was reduced to 12, all of the species were placed correctly with only difference being wrong insect and fish clusters switched. Then to in-paralogs matrix the neighbour-net algorithm was applied. The resulting "net" tree showed the species with fast or slow duplications rates compared to the others. We could identify species with very high or very low duplications frequencies and it correlates with known occurrences of the whole genome duplications. As the next step I built the graphs for every single species showing the correlation between their in-paralogs number and evolutionary distance. As we have 21 species, graph for every species is built using 20 points. Coordinates of the points are set using the evolutionary distance to that particular species and in-paralogs number. In mammals with increasing the distance from speciation the in-paralogs number also increased, however not in linear fashion. In fish and insects the graph close to zero is just the same in mammals' case. However, after reaching the evolutionary distances more than 800 million years the number of inparalogs is beginning to decrease. We also made a simulation of gene duplications for all 21 species and all the splits according to the fossil and molecular clock data from literature. In our simulation duplication frequency was minimal closer to the past and maximum in the near-present time. Resulting curves had the same shape the experimental data ones. In case of fish and insect for simulation the duplication rate coefficient even had to be set negative in order to repeat experimental curve shape. To the duplication rate coefficient in our simulation contribute 2 criteria: gene duplications and gene losses. As gene duplication is stochastical process it should always be a constant. So the changing in the coefficient should be solely explained by the increasing gene loss of old genes. The processes are explained by the evolution model with high gene duplication and loss ratio. The drop in number of in-paralogs is probably due to the BLAST algorithm. It is observed in comparing highly divergent species and BLAST cannot find the orthologs so precisely anymore. In the second part of my work I concentrated more on the specific function of inparalogs. Because such analysis is time-consuming it could be done on the limited number species. Here I used three insects: Drosophila melanogaster (fruit y), Anopheles gambiae (mosquito) and Apis mellifera (honeybee). After Inparnoid analyses and I listed the cluster of orthologs. Functional analyses of all listed genes were done using GO annotations and also KEGG PATHWAY database. We found, that the gene duplication pattern is unique for each species and that this uniqueness is rejected through the differences in functional classes of duplicated genes. The preferences for some classes reject the evolutionary trends of the last 350 million years and allow assumptions on the role of those genes duplications in the lifestyle of species. Furthermore, the observed gene duplications allowed me to find connections between genomic changes and their phenotypic manifestations. For example I found duplications within carbohydrate metabolism rejecting feed pattern adaptation, within photo- and olfactory-receptors indicating sensing adaptation and within troponin indicating adaptations in the development. Despite these species specific differences, found high correlations between the independently duplicated genes between the species. This might hint for a "pool" of genes preferentially duplicated. Taken together, the observed duplication patterns reject the adaptational process and provide us another link to the field of genomic zoology.},
  subject      = {Duplikation},
  language  = {en}
}
@phdthesis{Sieger2020,
  author    = {Sieger, Charlotte Sophie},
  title     = {Potential evolutionary responses to landscape heterogeneity and systematic environmental trends},
  doi       = {10.25972/OPUS-21669},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-216690},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2020},
  abstract  = {Over the course of the last century, humans have witnessed drastic levels of global environmental change that endangered both, the survival of single species as well as biodiversity itself. This includes climate change, in both environmental means and in variance and subsequently frequent extreme weather events, as well as land use change that species have to cope with. With increasing urbanization, increasing agricultural area and increasing intensification, natural habitat is not only lost, but also changes its shape and distribution in the landscape. Both aspects can heavily influence an individual's fitness and therefore act as a selective force promoting evolutionary change. This way climate change influences individuals' niches and dispersal. Local adaptation and dispersal are not independent of each other. Dispersal can have two opposite effects on local adaptation. It can oppose local adaptation, by promoting the immigration of maladapted indi- viduals or favor local adaptation by introducing better adapted genotypes. Which of those effects of dispersal on local adaptation emerges in a population depends on the dispersal strategies and the spatial structure of the landscape. In principle an adaptive response can include adjustment of the niche optimum as well as habitat tolerance (niche width) or (instead) ecological tracking of adequate conditions by dispersal and range shifting. So far, there has been no extensive modeling study of the evolution of the environmental niche optimum and tolerance along with dispersal probability in complex landscapes. Either only dispersal or (part of ) the environmental niche can evolve or the landscapes used are not realistic but rather a very abstract representation of spatial structures. I want to try and disentangle those different effects of both local adaptation and dispersal during global change, as well as their interaction, especially considering the separation between the effects of increasing mean and increasing variance. For this, I implemented an individual based model (IBM), with escalating complexity. I showed that both on a temporal as well as on a spatial scale, variation can be more influential then mean conditions. Indeed, the actual spatial configuration of this heterogeneity and the relationship between spatial and temporal heterogeneity affect the evolution of the niche and of dispersal probability more than temporal or spatial mean conditions. I could show that in isolated populations, an increase of an environmental attribute's mean or variance can lead to extinction, under certain conditions. In particular, increasing variance cannot be tracked forever, since increasing tolerance has distinct limits of feasibility. Increasing mean conditions can also occur too fast to be tracked, especially from generalist individuals. When expanding the model to the metapopulation level without a temporal environmental trend, the degree of spatial vs.temporal heterogeneity influenced the evolution of random dispersal heavily. With increasing spatial heterogeneity, individuals from extreme and rare patches evolve from being philopatric to dispersive, while individuals from average patches switch in the opposite direction. With the last expansion to a different set of landscapes with varying degrees of edge density, I could show that edge effects are strong in pseudo-agricultural landscapes, while in pseudo-natural habitats they were hardly found, regardless of emigration strategy. Sharp edges select against dispersal in the edge patches and could potentially further isolate populations in agricultural landscapes. The work I present here can also be expanded further and I present several suggestions on what to do next. These expansions could help the realism of the model and eventually shed light on its bearing on ecological global change predictions. For example species distribution models or extinction risk models would be more precise, if they included both spatial and temporal variation. The current modeling practices might not be suffcient to describe the possible outcomes of global change, because spatio-temporal heterogeneity and its influence on species' niches is too important to be ignored for longer.},
  language  = {en}
}
@article{HuebnerWissemann2004,
  author    = {H{\"u}bner, Stefanie and Wissemann, Volker},
  title     = {Morphometrische Analysen zur Variabilit{\"a}t von Prunus spinosa L. - Populationen(Prunoideae, Rosaceae) im mittleren Saaletal, Th{\"u}ringen},
  doi       = {10.3264/FG.2004.1215},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-35207},
  year      = {2004},
  abstract  = {Prunus spinosa L. (Rosaceae) is one of the most widespread members of the genus Prunus in middle europe. Its morphological plasticity resulted in a number of described taxa at subspecific level. Since the early neolithic times, drupes of the plum family are recorded and exhibit already a remarkable diversity in size and form. Here we present a short historical account to the use of P. spinosa and an overview of the different taxonomic treatments. We examined distribution patterns in general and in particular in the central valley of the river Saale (Thuringia) with respect to ecological, edaphic and climatic factors. We assessed within 16 populations the variability of 22 metric and 10 qualitative morphological characters at 7 different locations. Population sites included forest-, way- and fieldsides, as well as lightish pine forests. Pollen fertility did not increase during the flowering period, all flowers were directly fully fertile from the beginning. In contrast, glucose content varied significantly depending of the status of fertilization. Epicuticular wax structure was without variation amongst the populations. P. spinosa leaves are covered with a smooth layer of slightly striated wax. Morphological characters were scored on 270 branches and 506 fruits. Most of the characters showed enormous variability among and within populations such as metrics of leaves, thorns and character states of flower morphology. The lowest variability among populations and therefore not dependend of modificatory factors was found in fruit characters. Since kernel morphology seems to be genetically rather than modificatory controlled, we applied the 3 taxonomical concepts of Werneck, K{\"u}hn and Scholz u. Scholz to identify evolutionary units at subspecific levels. However, population variability was still so high, that from our study here we can not support an infraspecific classification of Prunus spinosa L.},
  subject      = {Prunus},
  language  = {de}
}
@article{SchneiderDobrindtMiddendorfetal.2011,
  author    = {Schneider, Gy{\"o}rgy and Dobrindt, Ulrich and Middendorf, Barbara and Hochhut, Bianca and Szij{\´a}rt{\´o}, Valeria and Em{\´o}dy, Levente and Hacker, J{\"o}rg},
  title     = {Mobilisation and remobilisation of a large archetypal pathogenicity island of uropathogenic \(Escherichia\) \(coli\) \(in\) \(vitro\) support the role of conjugation for horizontal transfer of genomic islands},
  series = {BMC Microbiology},
  volume    = {11},
  journal   = {BMC Microbiology},
  doi       = {10.1186/1471-2180-11-210},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-140975},
  pages     = {210},
  year      = {2011},
  abstract  = {Background: A substantial amount of data has been accumulated supporting the important role of genomic islands (GEIs) - including pathogenicity islands (PAIs) - in bacterial genome plasticity and the evolution of bacterial pathogens. Their instability and the high level sequence similarity of different (partial) islands suggest an exchange of PAIs between strains of the same or even different bacterial species by horizontal gene transfer (HGT). Transfer events of archetypal large genomic islands of enterobacteria which often lack genes required for mobilisation or transfer have been rarely investigated so far. Results: To study mobilisation of such large genomic regions in prototypic uropathogenic E. coli (UPEC) strain 536, PAI II(536) was supplemented with the mob(RP4) region, an origin of replication (oriV(R6K)), an origin of transfer (oriT(RP4)) and a chloramphenicol resistance selection marker. In the presence of helper plasmid RP4, conjugative transfer of the 107-kb PAI II(536) construct occured from strain 536 into an E. coli K-12 recipient. In transconjugants, PAI II(536) existed either as a cytoplasmic circular intermediate (CI) or integrated site-specifically into the recipient's chromosome at the leuX tRNA gene. This locus is the chromosomal integration site of PAI II(536) in UPEC strain 536. From the E. coli K-12 recipient, the chromosomal PAI II(536) construct as well as the CIs could be successfully remobilised and inserted into leuX in a PAI II(536) deletion mutant of E. coli 536. Conclusions: Our results corroborate that mobilisation and conjugal transfer may contribute to evolution of bacterial pathogens through horizontal transfer of large chromosomal regions such as PAIs. Stabilisation of these mobile genetic elements in the bacterial chromosome result from selective loss of mobilisation and transfer functions of genomic islands.},
  language  = {en}
}
@article{PoethkeHovestadtMitesser2003,
  author    = {Poethke, Hans-Joachim and Hovestadt, Thomas and Mitesser, Oliver},
  title     = {Local extinction and the evolution of dispersal rates: Causes and correlations},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-47718},
  year      = {2003},
  abstract  = {We present the results of individual-based simulation experiments on the evolution of dispersal rates of organisms living in metapopulations. We find conflicting results regarding the relationship between local extinction rate and evolutionarily stable (ES) dispersal rate depending on which principal mechanism causes extinction: if extinction is caused by environmental catastrophes eradicating local populations, we observe a positive correlation between extinction and ES dispersal rate; if extinction is a consequence of stochastic local dynamics and environmental fluctuations, the correlation becomes ambiguous; and in cases where extinction is caused by dispersal mortality, a negative correlation between local extinction rate and ES dispersal rate emerges. We conclude that extinction rate, which both affects and is affected by dispersal rates, is not an ideal predictor for optimal dispersal rates.},
  subject      = {Ausbreitung},
  language  = {en}
}