Secondary (and tertiary) structure of the ITS_1tn2 and its application for phylogenetic tree reconstructions and species identification [Elektronische Ressource] / vorgelegt von Alexander Keller

Sujets

• Biologie

Informations

• Publié par: julius-maximilians-universitat_wurzburg
• Publié le: 01 janvier 2010
• Nombre de lectures: 19
• Langue: English
• Poids de l'ouvrage: 16 Mo

Extrait

Secondary (and tertiary) structure of the ITS2
and its application for phylogenetic tree reconstructions
and species identification
vorgelegt von
Dipl. Biol. Alexander Keller
Würzburg, 2010
Kumulative Dissertation zur Erlangung des
naturwissenschaftlichen Doktorgrades (Dr. rer. nat.)
der Bayerischen Julius-Maximilians-Universität WürzburgEinreichung: in Würzburg
Mitglieder der Promotionskommission:
Vorsitzender: Prof. Thomas Dandekar
1. Gutachter: Prof.
2. Prof. Ingolf Steffan-Dewenter
Promotionskolloquium: in Würzburg
Aushändigung Doktorurkunde: ing
iiiTABLE OF CONTENTS
Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . vii
Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii
Zusammenfassung . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . ix
I General Introduction 1
II Materials and Methods 9
1 Materials 11
2 Bioinformatic tools 13
2.1 Annotation Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3 Bioinformatic approaches 15
3.1 HMM-Annotation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.2 Secondary Structure Prediction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
3.3 Tertiary Structure Prediction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
4 Phylogenetic procedures 17
4.1 Alignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
4.2 Substitution model selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
4.3 Tree reconstructions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
4.4 CBC analyses . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
4.5 Tree viewers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
5 Simulations 21
5.1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
5.2 Datasets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
5.3 Robustness and Accuracy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23
III Results 25
6 Contributions to the methodological pipeline 27
P.1 5.8S-28S rRNA interaction and HMM-based ITS2 annotation . . . . . . . . . . . . . 28
P.2 The ITS2 Dababase III-sequences and structures for phylogeny . . . . . . . . . . . 38
v7 Evaluation of secondary structure phylogenetics 45
P.3 Including RNA secondary structures improves accuracy and robustness in recon-
struction of phylogenetic trees . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
8 Phylogenetic case studies 59
P.4 ITS2 data corroborate a monophyletic chlorophycean DO-group (Sphaeropleales) 60
P.5 ITS2 sequence-structure phylogeny in the Scenedesmaceae with special reference
to Coelastrum (Chlorophyta, Chlorophyceae), including the new genera Comasiella
and Pectinodesmus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
P.6 Internal transcribed spacer 2 (nu ITS2 rRNA) sequence-structure phylogenetics:
Towards an automated reconstruction of the green algal tree of life . . . . . . . . . 86
P.7 ITS2 secondary structure improves phylogeny estimation in a radiation of blue
butterflies of the subgenus Agrodiaetus (Lepidoptera: Lycaenidae: Polyommatus) . 124
9 Secondary structure Phylogenetics in Ecology 153
P.8 Ant-flower networks in Hawai’i: native plants are exploited, introduced plants
defended . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
P.9 Composition of epiphytic bacterial communities differs on flowers and leaves . . 210
10 Future prospects of structural phylogenetics 229
P.10 Ribosomal RNA phylogenetics: the third dimension . . . . . . . . . . . . . . . . . . 230
IV General Discussion and Conclusions 235
V Bibliography and additional Information 245
Bibliography 247
Acronyms 273
List of Figures 275
List of Tables 279
Curriculum Vitae 281
List of Publications 283
Thesis Statistics 285
Erklärung 291
viACKNOWLEDGEMENTS
Preceding the actual thesis, I want to acknowledge the support of many persons that directly
or indirectly enabled me to manage the projects, and of course lately the final writing. First
to mention are my supervisors, Prof. Dr. Thomas Dandekar, Dr. Matthias Wolf, Prof. Dr. Jörg
Schultz and Dr. Tobias Müller, who designed interesting and prosperous projects for my
graduate studies and were always helpful, where needed. Further, I would like to thank all
the other companions of our working group on the way to the PhD: these were Dr. Frank
Förster, Tina Schleicher, Christian Koetschan, and the bachelor students Benjamin Merget
and Gregor Schalk. The remaining members of the Department of Bioinformatics can be
added to this list for all their fruitful discussions and useful ideas.
In addition to these persons of our department, I want to thank all my external collabo-
rators, which are Prof. Dr. Mark Buchheim, Dr. Martin Wiemers, Dr. Eberhard Hegewald,
Robert Junker, Dr. Nico Blüthgen, Christina Loewel, Prof. Dr. Curtis Daehler, Dr. Stefan
Dötterl, Prof. Dr. Thomas Friedl, Prof. Dr. Roy Gross, Prof. Dr. Lothar Krienitz, Katrin
Schlegelmilch, and Prof. Dr. Norbert Schütze, for all their efforts and their investments into
our collaborative projects. Furthermore, I would like to especially thank Prof. Dr. Ulf Sorhan-
nus as a collaborator and as a very obliging host (together with Prof. Dr. Marty Mitchell and
Linda Kightlinger) during my visit at the Edinboro University of Pennsylvania.
Many thanks for agreeing to review this thesis to my universitary advisory committee
Prof. Dr. Thomas Dandekar and Prof. Dr. Ingolf Steffan-Dewenter and as well the advi-
sory committee of my graduate school BIGSS consisting of Prof. Dr. Thomas Dandekar,
Prof. Dr. Jörg Schultz and Prof. Dr. Heinrich Sticht. For financial sponsoring and meeting
the costs of my travels and research equipment, I gratefully acknowledge the Elite Network
Bavaria graduate school BIGSS. Furthermore, as this thesis has been awarded with the Bio-
center Science Award, I would like to thank the Biocenter Würzburg Commitee for their
choice and I appreciate very much the interest in my work.
Especially, I am deeply grateful to my family including Katrin for supporting and encour-
aging me during the complete time of my studies; and even more for the reviving times
away from these! They and several good friends had to cope with less visits by me and
other cut-backs; I really appreciate your patience and hope to see you more in the time after
thesis submission!
viiSUMMARY
Biodiversity may be investigated and explored by the means of genetic sequence informa-
tion 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 comprehen-
sive 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 indepen-
dent phylogenies within the green algae that further corroborate the idea that secondary
structures improve the obtainable phylogenetic signal, but now from a biological perspec-
tive. 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 e