EES PhD Students 2011

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Sidonie Bellot

Supervisor: Susanne Renner
Title of thesis: Using next-generation-sequencing to study the organellar genomes of holoparasitic Pilostyles (Apodanthaceae) and to investigate horizontal gene exchange with its legume hosts.
Contact: Sidonie

Abstract: Most reports of natural horizontal gene transfer (HGT) in higher plants involve short fragments of mitochondrial DNA, usually taken up by parasitic species from their hosts. The first case of HGT involving a nuclear gene also comes from a parasite, namely Striga hermonthica (Orobanchaceae) and its monocot crop host Sorghum bicolor (Yoshida, 2010). These findings indicate that cell-to-cell contact between species provides a route for gene flow throughout cell boundaries. The amount of DNA that can be transferred and its organellar location in the receiving organism have not been studied. This is because until recently, the required deep sequencing of host and parasite DNA was not feasible at reasonable expense, and suitable pairs of holoparasites and hosts were not readily available in cultivation. Parasitism is found in only a handful of families of flowering plants, each time involving the ability to uptake water and nutrients directly from host’s tissues through specialized feeding structures. Some parasitic plants have even lost the ability to photosynthesize and grow nearly completely embedded within the host tissues as so-called endoparasites, emerging only during sexual reproduction (i.e., these parasites never produce leaves). This is the case for the Apodanthaceae, a small family that is a research focus in the Renner lab. It has been shown that Apodanthaceae belong in the Cucurbitales, and their organellar and nuclear genome can therefore in principle be compared to the completely sequenced genomes of several lines of Cucumis sativus. In my doctoral research, I plan to use next-generation-sequencing to address questions about molecular evolution in the organellar genomes of the endoparasite Pilostyles hamiltonii. My detailed work plan is not yet clear, but I will probably focus on the chloroplast genome and the most common types of repetitive DNA. Little is known about the changes in the chloroplast genomes of holoparasitic, hemiparasitic, and autotrophic species, except for ongoing work by S. Wicke and G. Schneeweiss, who have characterized the patterns of gene loss, modification, and transfer in the chloroplasts of Orobanchaceae. Both researchers will be collaborating with me. The repetitive DNA is of interest because I would like to compare the most abundant types of transposons with those found by M. Piednoel, a postdoc in the Renner lab focusing on the repetitive DNA of Orobanchaceae (DFG-RE 603/9-1), again in collaboration with G. Schneeweiss from the University of Vienna. To bring the host plant into cultivation in Munich, I will visit our Australian collaborator, K. Dixon, during the summer of 2011, who is studying the germination conditions of P. hamiltonii. My research will be the first ever such genome-level comparison and will provide insights both, into plastid genome evolution in holoparasites and into the extent of HGT between parasites and their hosts."

Andrea Biebl
Supervisor: Roland Melzer
Title of thesis: 3D-reconstruction and visualisation of the central nervous system of sea spiders (Chelicerata: Pycnogonida).
Contact: Andrea

Abstract: Pycnogonida (sea spiders) are a puzzling group of marine arthropods exhibiting various uncommon features, e.g. the prominent proboscis, the ovigers used by the males to carry eggs and the extreme reduction of the abdomen are some of their strange characteristics. They show a broad range of sizes, forms and habits. From tiny, short-legged intertidal species to large, and long-legged abyssal forms. They inhabit all marine benthic environments but tend to be enigmatic and infrequent. For a long time, they were supposed to be incertae sedis. There are three different views of their phylogentic position: either as sister group to the euchelicerates, with whom they share a chelate first appendage as a potential synapomorphy, or as a sister taxon to all other euarthropods, or even as rather derived chelicerates forming the sister-group of the Acari.

The aim of this study is taking a closer look on the nervous system with emphasis on the ventral ganglia of Pycnogonida using techniques, which have never been used before for studies on pycnogonids: computer based 3D-reconstruction of the nervous system based on semithin sections, paraffin histology and different stainings like Wigglesworth, reduced silver staining and anti-body staining . In general the results are compared with classical studies, but also with recent literature to compare the results with other arthropods.

Katharina Böndel
Supervisor: Wolfgang Stephan
Title of thesis: Sequence evolution of genes involved in abiotic stress tolerance in wild tomato populations using next-generation sequencing technologies.
Contact: Katharina

Abstract: The wild tomato species studied in this project are distributed along the west coast of South America. Their habitat range covers a lot of different environmental conditions: 1) from mesic in Southern Peru to very dry in the Atacama desert in Chile, 2) from sea level up to 3,500 m in the Andes and, 3) high salt concentrations in the soil at the Pacific coast. Thus, these species encounter several abiotic stresses like drought, salinity, and cold and this makes wild tomatoes an ideal subject to study local adaptation. The idea of this project is to sequence several genes from a pathway or gene network, which is mediating the abiotic stress response, from several populations of wild tomatoes. Since traditional Sanger sequencing does not allow gathering huge amounts of data, i. e. sequencing a lot of genes in a short time, next generation sequencing technologies will be applied. The aim of this project is to detect which evolutionary forces act where in this pathway, i. e. to detect differences between the genes, and also to detect differences between the populations and/or species.

Ana Catalan

Supervisor: John Parsch
Title of thesis: Analysis of sex-, tissue-, and population- specific gene expression in Drosophila melanogaster
Contact: Ana

Abstract: The main topic of my Ph.D is to study differences in gene expression between populations and its importance as a basis for adaptation. To study gene expression variation we use two populations of Drosophila melanogaster, one ancestral Zimbabwean population and a derived Dutch population that diverged around 15,000 years ago. To study differences on gene expression between Africa and Europe we use several techniques like microarrays, RNA-seq and quantitative RT-PCR. For example, from a whole genome microarray analysis of European and African D. melanogaster several genes were detected to be differentially expressed. One of these genes is foraging, which in the fly it is involved in processes like feeding behavior, memory and learning. We want to find out what are the genetic changes that cause the difference in expression observed in foraging from African and European flies and if this difference rose because of natural selective forces or demographic events. We also want to understand how gene expression levels influence a specific phenotype and how this phenotype-gene expression variation is important for adaptation.

Wolfgang Engelbrecht

Supervisors: Justyna Wolinska, Christian Laforsch
Title of thesis: Facing Multiple Enemies: Interactions between parasites and predators and the impact on the host/prey
Contact: Wolfgang

Abstract: Many organisms confronted with an everchanging spectrum and abundance of predators show inducible defences. This field has been studied intensively, but not much is known about the extent of impact a simultaneous exposure to enemies of other functional levels, such as parasites, has on these defences. In nature most organisms are exposed to more than a single threat from a defined functional level and all inducible defences have costs. Therefore there must be trade-offs between the different responses. In my work I look at the effects predators and parasites have on waterfleas when they are present at the same time. Since waterfleas exhibit a wide range of inducible defences ranging from behavioral to morphological changes and are also host to many parasites they provide many different possibilities for interactions and therefore are good organisms for my experiments.

Christian Foth
Supervisor: Oliver Rauhut
Title of thesis: Macroevolutionary patterns in the evolution of the skull in theropod dinosaurs: a morphometric approach.
Contact: Christian

Abstract: Theropod dinosaurs were one of the most conspicuous groups of terrestrial vertebrates during the Mesozoic, and, in the form of birds, this is true even today. Although their evolutionary history is thus of greatest importance for understanding the origin and evolution of one of the most diverse vertebrate groups today, studies of macroevolutionary patterns in theropods are still rare, especially for the evolution of the skull in this group. However, recent works on theropod skull ontogeny and biomechanics provide a good base for such studies. In the current project, I will investigate the evolution of the skull in non-avian theropods and basal birds, using a geometric morphometric approach. I will thus establish the morphospace occupied by theropod skulls and analyse shifts in morphospace during theropod evolution. By integrating these morphometric studies with results from analyses of theropod skull ontogeny and biomechanics, I will further investigate the influence of heterochrony and functional aspects on the evolution of the theropod skull. The project will thus lead to a much better understanding of macroevolutionary patterns in the evolution of theropod skulls on the lineage towards birds.

Michaela Gerges

Supervisor: Andreas Zahn
Title of thesis: Evaluation of riparian forests as guidelines and feeding areas in bat migration - a study for a sustainable development of riparian forests with regard to the conservation of species.
Contact: Michaela

Abstract: It is known that there are some bat species around the world that make seasonal migrations searching for hibernation sites or habitats with an abundant food supply. However, the routes taken by the bats and the cues used for orientation and navigation during their migrations are still unknown. In this context, one assumption is that rivers with their accompanying riparian forests are of great importance as guidelines for long-distance orientation and as feeding areas for migrating bats, but up to now there is little evidence to prove this assumption. Within the framework of my dissertation project, I am going to discuss the importance of rivers and their accompanying riparian forests for bat migration in the alpine range of southern Bavaria and northern Austria. In order to achieve this, I am going to investigate bat activity during migratory and nursery seasons at the rivers Inn and Salzach. The aims of the project are to support the idea that bats use rivers as landmarks while migrating to alpine hibernation sites and to evaluate local riparian forests as feeding habitats for bats during migration compared to ecologically similar habitats without proximity to rivers.

Quirin Herzog
Supervisor: Christian Laforsch
Title of thesis: Reversibilty of Inducible Defenses in Daphnia.
Contact: Quirin

Abstract: Phenotypic plasticity, apart from genetic adaptation, is an important and widespread response to changes in environmental conditions, such as predation. This highly variable and strong driving force of selection often causes prey to form so called 'inducible defences'. While both proximate and ultimate factors of inducible defenses have been intensivly studied, not much is known about the reversibility of those defenses. Therefore theoretical models provide the best assessment under which conditions inducible defences can be reversible. The aim of this phd-project is to provide empirical data to verify and specify the predictions made by theoretical models. I'll focus on Daphnia, a genus of model-organisms in the field of inducible defenses. In an initial step reversible and irreversible inducible defenses should be analysed and classified using modern imaging techniques such as phase-sensitive acoustic microscopy (PSAM) and optical coherence tomography. In the following I'll look at different factors such as the quality of signals (i.e. kairomones, microturbulences) or physiological costs and their influence on the reversibility of inducible defenses. The consequently obtained data should contribute to a basic understanding of phenotypic plasticity, which is a basic requirement of understanding how organisms can flexibly react to changes in their environment.

Olivia Hesse

Supervisors: Justyna Wolinska, Christian Laforsch
Title of thesis: Facing Multiple Enemies: Predator-Prey/Host-Parasite Interactions
Contact: Olivia

Abstract: Many organisms that face a continuously changing predator spectrum express inducible defences. Although inducible defences have been extensively studied, only little is known about these anti-predator adaptations in the context of simultaneous exposure to enemies from different functional levels, such as parasites. This is surprising, given that in nature, most organisms are exposed to a variety of enemies at the same time, leading to trade-offs between adaptive responses. I study the effects of such a multiple-enemy situation to explore how inducible defences and effects of parasitism might interact. As the target prey/host organism I use waterfleas (Daphnia) which respond to predator cues by forming defensive morphological structures such as helmets or elongated tail spines and by changing their behaviour or life histories. Also, Daphnia are hosts to a variety of parasites, making them the ideal model system for my study.

Hannes Imhof

Supervisor: Christian Laforsch
Title of thesis: Plastic particles in aquatic ecosystems: occurence and influence on aquatic organisms.
Contact: Hannes

Abstract: The pollution of marine environments with plastic waste is well documented since the last years. High amounts of particles have been accumulated in the sediments and in the pelagic zone and are ingested by many organisms. Therefore the plastic accumulates in the food chain and is getting a risk for humans and the environments. In contrast, only a few studies are known concerning the amount of discharged plastic particles to freshwater environments. There is a high requirement for scientific studies to examine the potential endangerment by plastic particles of these ecosystems. The Goal of my interdisciplinary study is to quantify the pollution with plastic particles of German and European lakes and streams and to assess the distribution pattern within the waters with the help of Raman-Microscopy (RM). In addition we will test for influences to freshwater environments. We will use chosen species as examples for different functional groups and test for accumulation of plastic particles in the organisms and furthermore for influences to life-history, reproduction and mortality. Next to sophisticated histological techniques, RM is used and further developed as an efficient method to show the ingestion and possible accumulation of plastic particles in organisms and organs in-vivo.

Kathrin Otte

Supervisor: Christian Laforsch
Title: Phenotypic plasticity in Daphnia: A ecological proteomic approach .
Contact: Kathrin

Abstract: Predation is a key factor in the evolution of prey species and the dynamics of prey communities. In both animals and plants, different defensive mechanisms have evolved in response to this selection pressure. Phenotypic plasticity in defensive traits appears to be an appropriate mechanism to cope with the variable hazard of a frequently changing predator system. A textbook example for these so called inducible defences is the waterflea Daphnia. However, our understanding of the mechanisms underlying plastic responses in Daphnia is still in its infancy. Given that Daphnia is emerging as the key model invertebrate system in ecological genomics, our study aims to discover the molecular basis of predator induced defences. Therefore, we will analyse conditionally expressed proteins in response to different predator regimes. As proteomic and transcriptomic approaches are complementary to relate gene expression data to the organism’s phenotype, our overall aim in this collaborative project is to combine both methodologies in the long run to gain insight into the evolution of genes involved in the formation of predator induced defences. This work is part of the EUROCORES STRESSFLEA Project granted by European Science Foundation.

Deborah Schweinfest
Supervisor: Volker Witte
Title of thesis: Selection pressures and adaptations in a multi-parasite system - a test of coevolutionary theory.
Contact: Debbie

Abstract: Colonies of the south-east Asian ponerine army ant Leptogenys distinguenda are inhabited by a diversity of symbiont species of different taxonomic groups that have evolved different behavioural, mechanical and chemical strategies to integrate into their host colonies. Living in or around the host colonies may provide several advantages for the symbiont species like protection from parasites and predators, stable environmental conditions and access to food. Previous studies revealed that many symbiont species of L. distinguenda behave parasitic in that some of them feed on the ant’s food resources (kleptoparsites) while others feed on the host’s brood. Thus, different parasite species impose differing fitness costs to their host. Fitness costs caused by parasites represent a selection pressure on the host species to evolve counter-adaptations in order to reduce the negative impact of the parasite. Frequent nest emigrations, the nest-mate recognition system and aggressive behaviour towards aliens might represent counter-adaptations against the different parasite species in the host ant L. distinguenda. However, given the differing impact of the parasite species, the question arises whether L. distinguenda applies a uniform defence strategy against all parasites or whether defence is adjusted to the impact of each parasite species. During my PhD thesis, I plan to study the impact of parasite species as well as the corresponding defence strategies used by the host ants.

Edwin Setiawan

Supervisor: Gert Wörheide, Dirk Erpenbeck
Title of thesis: Biodiversity and radiation of selected indonesian petrosiid sponges.
Contact: Edwin

Abstract: Indonesia is a ‘hotspot’ area for sponge biodiversity and therefore among the best regions to study their evolutionary/ biogeographic relationships. One of the most well known-sponge species in this region is Xestopongia testudinaria or the “giant barrel sponge”. The giant barrel sponge is not only a common reef dweller but also contains a wealth of bioactive compounds for potential pharmaceutical applications. Therefore, this species is also important for biopharmaceutical research. Another species, Neopetrosia exigua was regarded as a closely related sister-species of Xestospongia testudinaria and originally described as Xestospongia exigua. It likewise contains a broad range of potential bioactive compounds and is abundant in the Indo-Pacific region. Despite their ecological and economic importance, radiation patterns of both species or the probable presence of species complexes within these have not been investigated yet. My project comprises a comprehensive study using molecular methods with two different markers (mitochondrial and nuclear DNA) in order to provide a significant insight into the biodiversity and radiation of these important species.

Robert Sigl

Supervisor: Christian Laforsch
Title of thesis: Morphological plasticity and migration behavior in Acanthaster planci – Adaptation strategy and explanation for outbreaks?
Contact: Robert

Abstract: Population explosions (so called Outbreaks) of the starfish Acanthaster planci are one of the most important threats to coral reefs. Still, their causes remain subject to a couple of hypothesis and till now there is no overall explanation for their emergence. In this project we want to test a hypothesis for the emergence of secondary Outbreaks, which are by now explained by mass-recruitment out of primary Outbreak populations. We want to investigate the possibility, that secondary Outbreaks arise by a huge number of starfish migrating from one reef to the next. Doing this we suppose the starfish to show a certain degree of morphological plasticity due to food limitation on their journey between reefs. The main points of investigation are: Does A. planci show morphological plasticity (investigated using state of the art techniques with clinical magnetic resonance imaging and following 3D-reconstruction of inner organs to estimate their volume)? What are the maximum travel distances of A. planci? Are chemical cues responsible for the formation of aggregations of A. planci? Our results will contribute significantly to the understanding of the emergence of secondary outbreaks which are supposed to be more common then primary ones.

Aretuza Sousa

Supervisor: Susanne Renner
Title of thesis: Inferring karyotype evolution in angiosperm, focusing on polyploidy and sex chromosomes.
Contact: Aretuza

Abstract: From my M.Sc. thesis, I have expertise in the molecular cytogenetics of plants, including Fluorescent-in-situ-Hybridization (FISH) and other approaches that help us understand the evolution and behavior of chromosomes. In my doctoral research, I am going to use this expertise in new ways. One question I plan to address is the ancestral karyotype of the ancient monocot family Araceae, which has about xx species in xx genera (use Natalie’s number). This family presents a wide variation of chromosome number, and chromosome counts are available for most genera. The ancestral chromosome number suggested to the family is x = 7 (Petersen, 1989), and there are species with up to 110 chromosomes. Two main mechanisms are though to explain changes in chromosome number: polyploidy and aneuploidy, and the direction of evolutionary can be inferred with the help of a phylogeny. Based on the distribution of diploid chromosome numbers in the Araceae I want to test the hypothesis that the base number was x = 13 or 14, not x = 7, and that the number of chromosomes in several Araceae clades actually was reduced, not increased. If this were true, it would have important implications for our understanding of the (hypothetical) ancestral Araceae genome. I will use a recently proposed maximum likelihood approach (Mayrose et al., 2010) to infer the most likely direction of karyotype changes, and I a will also then try to test the inferred direction of change by FISH work on selected clades of closely related species. Another question I wish to pursue is the evolution of plant sex chromosomes. For this work I shall use a species in the genus Coccinia, which has the largest Y chromosome known in all flowering plants. I will micro-dissect this chromosome using micro-dissection, working together with Andreas Houben in Gatersleben, who is an expert in this method (Houben et al., 2001). This will enable the isolation of the Y chromosome not only for cytogenetic study, but also for sequencing. Sex chromosomes are poorly known in plants, and the only Y chromosome so far sequencing is that of the liverwort Marchantia polymorpha (Okada et al., 2001). My study of the Coccinia grandis Y chromosome will contribute to a better understanding of the kinds of coding and non-coding DNA that makes up plant sex chromosomes.

Susanne Voigt
Supervisor: Wolfgang Stephan
Title of thesis: Looking for positive selection in Drosophila melanogaster.
Contact: Susi

Abstract: By means of population genetic and functional analysis, I try to detect positive selection that acted in the evolutionary history of the fruit fly Drosophila melanogaster. I am particularly interested in how the species managed to adapt to temperate climates after spreading from its Afrotropical origin to new territories. Therefore, I compare an African and a European population sample to find evidence of selection. In my current project, I have found a selective sweep in the European population by sequencing and population genetic analysis. Two genes in this sweep region are known to be differentially expressed between the African and European population samples and near to these genes the European sample harbors fixed SNP alleles which are not present in the African samples. Via functional analyses, I try to link these fixed differences between the samples to their different expression patterns of the before mentioned genes.

Andrea Weis

Supervisor: Roland Melzer
Title of thesis: Morphological and molecular studies on Chilean Pycnogonida.
Contact: Andrea

Abstract: The pycnogonida or sea spiders are an extraordinary group of exclusively marine arthropods. I am studying pycnogonid fauna of the Antarctic since 2008 and expanded my field of research also on the Subantarctic area in 2010. Now for my PhD Thesis I am focusing on the Chilean fjord region by analyzing samples collected from Huinay Scientific Field Station expeditions. Since most scientists focus on the Antarctic pycnogonid fauna the aim of my project is to extend the spectrum on hitherto relative unexplored regions. An interesting area is therefore the Chilean fjord region with its specific abiotic factors as well as impressive and unique benthos communities. Aim of my project is to create for the first time an atlas of the pycnogonid fauna from the Chilean fjord region. Beside classical light microscopical methods the scanning electrone microscope is used to study species specific sets of characters in detail. My second methodological approach focuses on the molecular taxonomy of these pycnogonids using CoI sequences.