Suggestions for Master's projects

Animal Behaviour

Adaptations to Population Densities in House Mice

Many parameters are expected to be different for mice in low densities compared to mice in high densities. For example, the frequency of females mating with multiple males. This has consequences for the optimal energetic investment and behaviour of males, e.g. do males with high investment into sperm production have more offspring in dense populations? We want to measure differences between mice in varying population densities to test hypotheses that are developed together. The MSc student will collect their own data and will be working with a PhD student who will set-up enclosures.
Contact: Jan-Niklas Runge  PD Dr. Anna Lindholm     Detailed information (PDF, 3288 KB)

 

The role of maternal effects in learning and innovation in Japanese quail

The ability to respond to environmental change and novelty has been suggested to be a main driver in the evolution of enlarged brains and its associated enhanced cognitive performance. Indeed, comparative analyses in birds and primates revealed that species with a relatively large brain have increased innovative abilities and are more likely to successfully establish themselves in novel environments. Within species, however, the evolutionary processes that shape individual variation in brain size and cognition remain poorly understood. In many taxa, a within-family resemblance in problem-solving abilities is observed. However, it is largely unclear if this within-family resemblance is due genetic or non-genetic effects. Using repeated Japanese quail (Coturnix japonica) selection lines for high and low maternal egg investment you will test how prenatal maternal investment influences brain development and cognitive performance in the offspring. This project will shed new light on the question what shapes and creates individual variation in cognitive ability within a species. It is ideal for a student who is interested in animal behaviour and evolutionary biology, and would like to spend a substantial amount of time doing practical work (innovation and other cognitive tests) with quails.
Contact: Prof. Dr. Barbara Tschirren    last update: 2014-05-14

 

Mate choice and genetic variation at ‘love hormone’ genes in Japanese quail

Studies in rodents have shown that the strength of pair bonding is influenced by genetic variation at the oxytocin (‘love hormone’) locus. Japanese quail differ in the strength of preference for their breeding partner in mate choice trials. Does genetic variation at bird ‘love genes’ explain these differences in partner preference? In this project you will perform mate choice tests with Japanese quail. In the lab, you will sequence the mesotocin and vasotocin locus (oxytocin-like hormones in birds) and test statistically if genetic variants at these loci are associated with the strength of partner preference in mate choice trails. This project is ideal for a student who is interested in behavioural genetics and would like to spend a substantial amount of time doing practical work with quails (mate choice tests) as well as genetic analyses in the lab.
Contact: Prof. Dr. Barbara Tschirren    last update: 2014-05-14

 

How to find a cooperative partner

Wild female house mice sometime cooperate to rear litters of pups. Partner choice is important, as lab studies have shown that a poor match can result in reproductive failure. How do females choose social partners for cooperative maternal care? Do they choose based on familiarity, genetic relatedness, extent of previous association, physical characteristics, or other characters? How much does partner choice influence reproductive success in a wild population?
In this project relevant data will be collected from a wild house mouse population near Zürich that is intensively monitored. Using the collected data, as well as data already available, the effect of the above factors on communal nursing partner choice will be assessed. An experiment will then be designed to test in the laboratory the factors which are found to have the largest effect on wild mouse female social partner choice.
Contact: Dr. Anna Lindholm  Prof. Dr. Barbara König 

 

Genetics and social behaviour of wild house mice

In Switzerland, house mice populations differ in the number of chromosomes, from 22 to 40. When mice with different numbers of chromosomes mate, then inviable offspring are likely to result. Two consequences are that females should have a mate preference for males which will give them viable offspring, and gene flow between populations of different chromosome numbers should be restricted.
This leads to a number of questions. How does a male’s chromosome number influence female mating preference? How does female reproductive success vary with the compatibility of her and her mate’s number of chromosomes? Can this explain the extent of genetic differentiation between house mouse populations?
In this project, wild mouse from populations near Zurich will be captured, brought to the lab, karyotyped, and genotyped. Mating crosses will be carried out, and female preferences will be tested using a sophisticated choice test apparatus. Population differentiation at neutral microsatellite markers will be assessed, and related to the outcome of mating crosses, and female preference tests.
Contact: Dr. Anna Lindholm  Prof. Dr. Barbara König

 

Automated observation of behaviour

Quantitative measures of the behaviour of many individual organisms over long durations can be very labour intensive, often prohibitively so. Yet such measurements can be the foundation of understanding how organisms interact with their environment, with each other, and how they respond to changing environmental conditions. The project will involve development and testing of a system for automating the process of observing and quantifying the behavioural characteristics of many individuals of different species simultaneously. Small aquatic organisms will be the model system used for development. The project will be of most interest to students with a strong interest in technical development, computational analyses, and organismal biology.
Contact: Prof. Dr. Owen Petchey    last update: 2012-09-28

 

Ecology and Environment

The genetic basis of adaptation to climate

For species found in temperate areas and mountainous regions, a major component of climate adaptation is the ability to withstand freezing temperatures. The plant species Arabidopsis thaliana is especially well-suited for investigating temperature adaptation. First, like other plant species, A. thaliana is immobile and almost certainly adapts to local temperatures. Moreover, A. thaliana is the plant genetic model species because it easy to use in genetic analyses.

We recently found evidence that the genetic bases of freezing tolerance differ across the range of A. thaliana. In this project, you will extend this research by investigating how differences in climate (e.g. temperature, precipitation) differentially shape freezing tolerance in distinct populations. What’s more, you will have an opportunity to investigate promising candidate genes in functional analyses. This project is an excellent opportunity for a student interested in climate adaptation and becoming familiar with statistical analyses, experimental design, and molecular genetics.
Contact: Dr. Matthew Horton  (matthew.horton at botinst.uzh.ch)  Department of Plant and Microbial Biology

 

Strigolactones as regulators of the rhizosphere microbiome

Strigolactones are newly discovered plant hormones that regulate plant morphology. In addition, they act as signaling compounds and initiate colonization by arbuscular mycorrhizal fungi (AMF), beneficial soil fungi that form symbiotic associations with plant roots and enhance plant growth. However, plant roots not only associate with AMF, but interact with a wide range of other microbes, some of them beneficial for plant growth and health. These other microbes may also use SLs as chemical cues to colonize roots.

In this project, we will use next generation sequencing to unravel the effects of strigolactones on the assembly of the rhizosphere microbiome in a range of plant species and using plant lines varying in strigolactone exudation. This master involves the following tasks: plant growth, molecular work (DNA extraction, PCR, preparation of sequencing library) and sequence data analysis with state-of-the-art bioinformatics and statistics.
Contact: Prof. Dr. Marcel van der Heijden (IEU, University of Zurich; Agroscope ISS)  Dr. Natacha Bodenhausen (Agroscope ISS) more details about the study:Rhizosphere ecology (research team), Plant-Soil-Interactions (research group), Agroscope Institute for Sustainability Science (ISS), 8046 Zürich-Affoltern   last update: 2015-08-19

 

Reconstruction of the Trifolium root microbiome

Plants host at their roots a diverse microbiota that is dissimilar from the sur-rounding soil microbial community (1). Such root-associated microbes include rhizobia or mycorrhiza, both well known for their host services, but, what is the role of the other root-associated microbiota members (2)? We have deter-mined the community composition of the root-associated bacterial microbiota of Trifolium and secondly, we have built a large culture collection of root-associated bacteria from red clover grown in natural soil under controlled conditions. The goal of this master project is to reconstruct the root bacterial community with the culturable bacterial strains and to test their potential to promote plant growth using a soil-like gnotobiotic system. The project com-prises in-vitro bioassays to quantify plant biomass using individual strains and the reconstructed synthetic community. Subsequently, we will manipulate the diversity of the synthetic community i.e. testing the consequences of species loss or complementation and synergism among different lineages. This work presents a step-change as host services are studied in a community context and we expect to obtain first insights how plants take advantage from their associated microbiome.
Contact: Klaus Schläppi (klaus.schlaeppi@agroscope.admin.ch)  Marcel van der Heijden (marcel.vanderheijden@agroscope.admin.ch) link: www.agroscope.ch/rhizosphere-ecology    last update: 2014-09-22

 

Amphibian conservation biology – Consequences of translocations:

Translocations are often used in conservation practice to rescue populations threatened by development or to create new populations. The currency for measuring the success of translocations is whether translocations led to a new population. Here we seek a master student who is keen to assess the success of a Natterjack toad translocation project. A previous master thesis showed that natural and translocated populations do not differ in microsatellite genetic variation. The aim of this project is to investigate phenotypic (i.e. fitness-related) traits using a common garden experiment in outdoor mesocosms. Eggs from different populations have to be collected in the wild. Tadpoles will be raised in captivity. As this study involves live individuals of a threatened species, we are looking for a highly motivated student who can handle animals carefully. For this master project, you need a driving license (field work). German is an advantage.
Contact: Dr. Benedikt R. Schmidt  

 

Amphibian conservation biology – The slow decline in abundance of a neglected species:

Conservation biologists usually study rare and enigmatic species. There is, however, a growing number of studies which shows that many other species, including common ones, are declining as well. The amphibian monitoring of the Swiss canton Aargau showed that the Palmate newt, Lissotriton helveticus, has been declining in abundance for the past ~15 years while pond occupancy remained roughly constant. Here we seek a master student who is keen to analyse the data using state-of-the-art statistical methods. The goal is a robust quantification of the decline. In addition, we would like to understand the reasons for the decline (land use change? climate change? a hoax?). Field work will be necessary to collect data which will then be used to test some hypotheses. For this master project, you need a driving license (field work). German is an advantage.
Contact: Dr. Benedikt R. Schmidt  

 

Niche differentiation in a model plant community and its genetic bases

In this interdisciplinary project, you will examine the genetic basis of diversity effects in simple plant communities. Recent ecological research has shown a positive relationship between diversity (i.e. species or genotypic diversity) and ecosystem functioning (e.g. productivity or stability of communities). A possible cause of diversity effects is niche partitioning amongst members of a community. Most species included in ecological studies are not genetically tractable, meaning that little reference to the genetic causes of such diversity effects can be made. Here, you will make use of the excellent genetic resources available for the plant Arabidopsis thaliana, such as natural accessions collected from all over the world. In an ongoing project, we have shown that certain combinations of accessions yield diversity effects. For these accessions, powerful genetic mapping populations exist and can be used for a genetic dissection of diversity effects. You will carry out greenhouse experiments to test whether variation in the ecological niches between individuals can be assessed through quantitative genetics.
Contact: Dr. Samuel Wuest    last update: 2013-09-13

 

Diversity effects along genetic gradients

Recent ecological research has frequently shown a positive relationship between species diversity or genotypic diversity and ecosystem functioning such as productivity or stability of communities. In agricultural reality, however, trends have increasingly been towards monoculture systems that rely strongly on high inputs and unsustainable use of pesticides. Increasing genetic diversity in agricultural systems has, in some cases, led to spectacular benefits for farmers and the environment – e.g. a drastic reduction in pesticide use or increased productivity. Studies of the fundamental principles underlying such diversity effects are needed. This project aims to use genetic variation gradients to partition such genetic diversity effects: How much of the diversity effects can be attributed to an increased number of alleles in populations, or alternatively, to increased number of genetic recombinants? You will perform greenhouse experiments to estimate the strengths of these different effects, and compare them to those of hybrid vigor (i.e. the use of hybrid plants that show greatly increased productivity) which is commonly used in agriculture.
Contact: Dr. Samuel Wuest    last update: 2013-09-13

 

How do mother plants count their offspring ?

Flowering plants exhibit extended maternal care, as mother plants are connected to the seed through a placenta. The developing seed is provided with nutrients for growth over an extended period of time. In order to maximize fitness in a given environment, a mother plant has thus to finely balance the investment of resources either to developing seeds or to the production of new reproductive units (the flowers). Interestingly, upon the production of a certain number of seeds (and under given growth conditions) the mother plant will terminate growth and stop the production of new flowers. It would appear that mechanisms exist through which a mother plant can count developing seeds and integrate this information with the amount of resources available.
The aim of this project is to describe how environmental and genetic variation affects offspring number through these mechanisms. In the project, you will be able to integrate methods from both ecology and genetics, through the use of natural genetic variation and environmental gradients. You will measure variation in resource allocation towards vegetative and reproductive structures in greenhouse experiments. The project could also include molecular analyses if desired.
Contact: Dr. Samuel Wuest    last update: 2013-09-13

 

Why are plant competitive interactions distance-dependent?

Plant competitive interactions decrease with distance, i.e. plant compete more intensely the closer they are. Interestingly, plant individuals of the same species compete over longer distances than individuals of different species, i.e. intra- and interspecific competition show different distance-dependencies. While this may be a mechanism promoting species coexistence, the underlying mechanisms are largely unknown.
This project will aim at disentangling these mechanisms by manipulating components of plant competition in experimental greenhouse ecosystem. This includes soil nutrient mobility and interactions over soil mycorrhizal networks. Methodologically, this will involve measurements of plant growth and the use of isotopes to trace nutrient movement in the model ecosystems.
Contact: PD Dr. Pascal A. Niklaus    last update: 2012-10-01

 

Physiological mechanisms underlying the growth/predation risk tradeoff

Prey animals defend themselves against predators, and usually pay a cost of that defense. Where does the cost come from? The traditional view assumes that prey reduce their foraging activity when they detect predators, therefore consuming less food and growing more slowly. But recent results call this view into question, and suggest instead that physiological changes in prey may be involved. This project will experimentally study the physiological responses of tadpoles (metabolic, digestive, hormonal) to predation risk over different time scales. The results will provide novel insight into mechanisms underlying the tradeoff between growing fast and avoiding predators.
Contact: PD Dr. Josh Van Buskirk    last update: 2012-09-26

 

Feedback between herbivores and their prey

In 1960, Nelson Hairston and colleagues published a paper that famously asked the question "Why is the world green?" Many possible answers have been provided over the decades since, but in fact we really don't know why herbivorous animals don't eat up all their prey. Plants do what they can to defend themselves from herbivores, but perhaps herbivores actually have positive indirect effects on their victims. This project will perform experiments with tadpoles and algae in artificial ponds to estimate several different kinds of effects of herbivores on plants, including direct consumption, nutrient recycling, and physical wounding and reduction of self-shading. If successful, this will be the first estimation of these effects within the same system, and will therefore represent a big step toward answering Hairston's question.
Contact: PD Dr. Josh Van Buskirk    last update: 2012-09-26

 

Influence of climate change on the timing of bird migration

Many recent studies report that songbirds in the Northern Hemisphere have begun their northward spring migration earlier during recent decades. Presumably, this is caused by increasingly warm spring temperatures. It is not known whether this trend is equally strong for all species, time periods, or geographic regions. We have a database containing all published data from long-term studies of the timing of bird migration.
You will update this database, and use meta-analyses to discover whether the shift varies among geographic regions and across different time periods. Are climatic variables associated with spatial and temporal variation? You will gain experience in planning, organizing, and statistically analyzing a large dataset.
Contact: PD Dr. Josh Van Buskirk  last update: 2012-09-26

 

Restoration through Rewilding: farce or fact?

The project focuses on finding better ways to restore damaged natural systems. Those who rehabilitate degraded lands or reintroduce endangered species must offer a rationale for choosing the target conditions they intend to bring back. But the increasing novelty of ecosystems (because of climate change and invasive species) means that restorationists cannot often use archival and paleoecological data to elucidate target states. They may therefore rely on non-historical rationales for justifying restoration's target conditions. "Rewilding" is an increasingly popular pursuit that requires us to identify optimal wild conditions, as through public surveys or locating reference states. A relevant field site and current restoration project will be studied, within Switzerland or beyond. Key questions include:

  • How can knowledge about the history of a site or species improve its restoration?
  • How can the appreciation of the past (historical sensitivity) improve the practice of restoration?
  • Has wilderness become a modern sacred site?
  • How do linguistic interpretations of "wilderness" in non-English languages affect the practice of rewilding?
  • See our Wilderness Babel

Contact: PD Dr. Marc Hall    last update: 2014-10-24

Linking ecosystems and human health: malaria control

Ecohealth experts and disease ecologists call attention to the ways that polluted and transformed ecosystems can adversely affect human health. This project explores the relationships between healthy ecosystems and healthy bodies by focusing on the methods of combating malaria, the world's second most deadly killer. Draining wetlands and spraying pesticides kill malaria's mosquito vector, but such activities also alter food webs, modify biodiversity, and threaten human physiology. This project focuses on the Swiss experience with battling malaria during the early 20th century, focusing on the Magadino Delta, Ticino. Sources of information include health experts and ecologists, local archives and libraries, the Swiss Tropical Institute, Basel, and WHO, Geneva. Questions might include:

  • What effects did early malaria control in Ticiono have on the local ecosystems?
  • How did Swiss malariologists utilize ecological principles in their projects?
  • How did antimalarial medications disrupt human health?
  • Can physicians and conservationists today agree that DDT and other powerful pesticides are effective for eradicating global malaria?

Contact: PD Dr. Marc Hall    last update: 2014-10-24

Invasive alien species: past experience for future management

Plants and animals from afar are transforming ecosystems while changing human societies, for worse and perhaps for better. Recent imports (such as Solidago) exacerbate human allergies or facilitate the spread of disease (as in the case of Aedes albopictus), but many of our most valuable agricultural crops are also alien and sometimes invasive. There is therefore an enormous need to evaluate the invasives, understand their impacts and learn how to manage them. While ecologists study biological relationships of these organisms, there remain surprisingly few studies that address political, social, and historical effects of these creatures. This project thus focuses on these human issues as by consulting experts or interest groups, by searching through natural and human archives, and doing field work. Collaboration with other researchers is encouraged. The following are a sampling of relevant invasive species questions:

  • How have botanical gardens contributed to the spread of alien invasives, and what measures can be used to control them?
  • In which instances have alien invasives been used to contribute to biodiversity protection?
  • What have been the bureaucratic and political challenges to importing analogue (alien) species, such as tortoises in Mauritius, where such organisms are replacing their extinct forerunners?
  • Biocontrols are species imported to control other noxious species. How have cautions over the use of biocontrols changed in the last few decades?

Contact: PD Dr. Marc Hall    last update: 2014-10-24

Food webs, foraging behaviour, and allometric scaling

Food webs, foraging behaviour, and allometric scaling are coming together to create a new and exciting frontier of research in ecology. This frontier aims to help understand the forces that structure ecological communities, and to provide an empirically evidenced theoretical foundation for predicting effects of environmental change on ecological communities. Relevant environmental changes include extinctions, invasions, temperature fluctuations, and habitat loss. The project will involve researching any of several new ideas in this field, and will suit students with a strong interest in coupling empirical data with theoretical models, and students that have the ability to think broadly and imaginatively while still focusing on a specific research question.
Contact: Prof. Dr. Owen Petchey  Interested students could start by reading an article in Functional Ecology   last update: 2012-09-28

 

What determines how fast I eat? Biotic and abiotic influences on feeding rates of aquatic organisms

Understanding how fast organisms eat is key for understanding the dynamics of predator-prey interactions. All sorts of factors can affect feeding rate, and during this project you will conceive, design, perform, and analyse experiments with small predators in lab-based communities. These predators are, despite their small size, quite impressive and voracious consumers! Which factors are investigated, such as prey identity, temperature, and disease, will be decided in collaboration with Owen. Depending on your interests, the project could include modelling of the dynamic consequences of your findings.
Contact: Prof. Dr. Owen Petchey  For an example of the kinds of results and conclusions that a similar study found, take a look at this paper   last update: 2012-09-28

 

Evolutionary Biology

Condition dependence of male courtship

Males developing under nutritional stress have fewer resources to invest as adults, which can affect their mating success and ultimately their fitness. Using well-studied genetic lines of Drosophila melanogaster, we will test how food stress during larval development affects male wing morphology. Since the wings play a critical role in courtship (including song production), we will further examine how condition-dependent wing morphology influences courtship song characteristics and ultimately male mating success.
Contact: Dr. Stefan Lüpold

 

Context-dependent female mate choice

Many studies assume that males vary in their genetic quality and that females choose males of the highest quality to gain genetic benefits for their offspring. However, it remains almost entirely unstudied to what extent such decisions are influenced by differences in the quality of the females themselves. Using genetic lines of Drosophila melanogaster, in which males produce glow-in-the-dark sperm, we will study the variation in female preference for males both before and after mating.
Contact: Dr. Stefan Lüpold

 

Epigenetic transmission of male quality effects

Classic sexual selection models often predict a genetic link between males’ sexually selected traits and their underlying genetic quality, rendering such traits honest signals of genetic quality to females. However, more recent models propose that the effects of male condition on offspring quality can also be non-genetic (or epigenetic). This project will follow the genetic and non-genetic effects of male quality across generations and determine their fitness consequences in Drosophila melanogaster.
Contact: Dr. Stefan Lüpold

 

Sexual selection in a species with extreme sexual dimorphism

This project examines how intra- and intersexual selection may shape the evolution of morphological and behavioural characteristics in Drosophila prolongata, a completely understudied species with extreme sexual dimorphism (including greatly exaggerated forelegs in males), elaborate courtship, and aggressive behaviour among males.
Contact: Dr. Stefan Lüpold

 

Foraging behaviour in a ground nesting passerine

This project studies foraging behavior of the red-listed wood warbler in the Swiss Jura mountains by means of radio-tracking to understand the key resources preferred during foraging. Field work April-July 2017.
Contact: PD Dr. Gilberto Pasinelli  

 

Effects of human-caused disturbances on bird behavior

This project addresses the role of short human-caused experimental disturbances on behavior and reproduction of birds equipped with radio transmitters.Field work March-July around Sempach (LU).
Contact: Dr. Susi Jenni  

 

Seasonal variation in woodcock calls

The project aims at examining the stability of woodcock calls throughout the breeding season. Calls of radio-tracked individuals will be recorded several times in the Jura moutains. Field work April-Juli 2017.
Contact: Pierre Mollet  

 

Impact of climate change on snow finches

The project investigates the links between environmental temperature, food availability, reproductive behavior and nestling growth in a habitat specialist in the Swiss Alps. Field work May-July, Furka (VS).
Contact: Dr. Fränzi Korner-Nievergelt  

 

Impact of avian malaria on bird migration patterns

By means of a systematic literature review and meta-analysis, this project elucidates the influence of avian malaria for migration patterns, for reproduction and survival in migratory birds. The project can be started anytime.
Contact: Dr. Silke Bauer  

 

Use of stop-over sites by migratory species

The project examines how migratory bird species use stop-over sites, what habitats they use, how long they stay, etc. using a systematic literature review and meta-analysis. The project can be started anytime.
Contact: Dr. Silke Bauer  

 

Forest tree genetics

Do central silver fir populations harbor more genetic diversity than marginal populations? Contrasting theory with data.

European silver fir (Abies alba Mill.) grows in many mountain ranges of Europe. Its current distribution range has been shaped by post-glacial re-colonization and recent land-use and climate change. As a result, silver fir has a fragmented distribution in the southern regions while it maintains continuous large populations in the central Alps and the Jura mountains, providing an ideal case study for testing hypotheses about marginal vs. central populations.

Population genetic theory predicts that populations at edges of the species range exhibit lower genetic diversity and greater genetic differentiation due to smaller effective population size and greater geographic isolation in comparison to geographically central populations. However, this prediction remains poorly tested due to many technical constraints and many processes (gene flow, demography, history) may cause differences between central and marginal populations.

Questions:

  • How to define marginality and centrality of a population?
  • How to simulate expected levels of genetic diversity at neutral loci depending on patch size, demographic history (e.g. distance from glacial refuge) and barriers to gene flow (such as mountains)?
  • Contrast simulated vs. real data to test if marginal populations have lower genetic diversity and greater genetic differentiation than central populations.

Available data: Over 70 silver fir populations across the distribution range, with 20 individuals genotyped at 500 SNP loci in each population.

Required skills: Interest in population genetics and in fundamental research, programming skills in R, experience with GIS tools (e.g. in R and with QGIS).

You will be supervised by Prof. Frédéric Guillaume (UZH) and Dr. Katalin Csilléry (ETH & WSL), and advised by Dr. Felix Gugerli (WSL). You will work in collaboration with two other Master’s students based at the WSL: one of them will develop a more precise distribution and abundance map of silver fir, and the other study adaptive divergence in the Swiss populations.
Contact: Katalin Csillery  Prof. Dr. Frédéric Guillaume

 

Rapid regulatory change: Tandem Repeat Variation at Transcription Factor Binding Sites

Much of the phenotypic variation that is observed among closely related species stems from changes in the level, timing, or location of gene expression. Sequence-specific binding of transcription factors to the regulatory regions of DNA is a key mechanism that determines gene expression, and mutations to these regions are a driving force in the evolution of gene expression patterns. Comparative genomic studies in eukaryotes provide evidence for rapid gain and loss of transcription factor binding sites (TFBSs). While single nucleotide polymorphisms and transposable elements are better studied in the context of TFBS evolution, a third class of variants, tandem repeats remain largely unexplored.
Tandem repeats (TRs) are stretches of DNA that are extremely variable in length and mutate rapidly. Human promoters are enriched in TRs, and their presence in regulatory regions greatly increases the divergence of gene expression profiles across human and other species. Yet, we do not have a clear understanding of the underlying mechanism. One plausible hypothesis is that TRs alter transcription factor binding profiles on regulatory regions. Indeed, several candidate gene studies in humans reported TR variations that modulate the binding of transcription factors, suggesting that rapid evolution of TRs might be contributing to TFBS evolution. By using genomics data on transcription factors and tandem repeats, we study the evolutionary dynamics of TR variations on transcription factor binding sites. The project aims to answer several questions:

  • Which TFBSs contain tandem repeats?
  • How many of these repeats are polymorphic?
  • What are the characteristics of these repeats?
  • Which are the genes that have TFBSs with polymorphic repeats?

Contact: Dr. Tugce Bilgin Sonay  Dr. Joshua Payne

 

Experimental Projects with Tribolium castaneum

  • Effect of genetic diversity on adaptation to changing environments

You will design an experiment to test the effect of reduced genetic diversity on the survival probability of experimental lines adapting to a new environment, over multiple generations. Following Fisher's Fundamental Theorem of adaptation, populations with reduced genetic diversity have a reduced rate of adaptation to a novel environment than populations with more variation. Because genetic diversity is a function of both population size and the degree of inbreeding of the individuals, the rate of adaptation, together with population extinction, must depend on two parameters: size and inbreeding level. Inbred populations further suffer from decreased fitness due to inbreeding depression, and should thus have higher risks of extinction than outbred populations of the same size. The experiment will tease apart the effects of population size and inbreeding on the time to extinction of replicate lines in two different environments. Preliminary results show that inbreeding has a strong effect on line survival rates. In this project, you will learn about experimental design, data analysis, the biology of T. castaneum, and the analysis of genetic data based on microsatellites to measure genetic diversity.

  • Effects of changing environments on fitness components

This project aims at finding which are the components of fitness most affected by stressful conditions (here, high temperatures and low humidity). Individual fitness is the trait under natural selection and is notoriously difficult to measure. Nevertheless, investigating levels of local adaptation in populations experimentally evolved to new environments necessitates to identify the best fitness proxies. Those proxies are the components of fitness that best predict total fitness. You will design an experiment enabling you to measure fitness components and total fitness (number of reproducing adults per female) by monitoring the developmental trajectories and survival probabilities of single individuals within full-sib families in different environments. By measuring the performances of offspring within families split among environments, you will be able to expose life-history trade-offs between, e.g., reproductive, developmental, and survival traits. You will also be able to indirectly measure the strength of selection acting on the measured traits by monitoring the change in their genetic and phenotypic variation. Additionally, you will have the opportunity to perform similar measurements in experimental lines currently evolving in the same test environments and thus demonstrate whether the measured traits have evolved in the direction of the selection inferred from your experiment. Finally, in this project, you will learn about experimental design, data analysis, and quantitative genetics. The project will allow you to understand the basics of experimental evolution and develop your skills in experimental data analysis and quantitative genetics theory.
Contact: Eva Koch (PhD student, direct supervisor, Y25-G-66c) Prof. Dr. Frédéric Guillaume (Y25-G-78) Evolutionary Genetics and Eco-Evolutionary Modelling Group (Guillaume Lab)   last update: 2015-08-24

 

The Genetics of Giants: Population- and Individual-level Genetic Variation in Aldabra Giant Tortoises

Aldabra, located in the western Indian Ocean, is home to a long-term study of the last surviving natural population of giant tortoises (Aldabrachelys gigantea). Although giant tortoises once dominated many island ecosystems, Aldabra is now the only place in the world where they occur in very large numbers. However, the population passed through a bottleneck of unknown magnitude around 120–150 years ago. As a consequence, all tortoises alive today descended from a small number of founders, some of which potentially survive to this day.

Over the past years, we have collected blood samples for hundreds of giant tortoises. In addition to these samples, we have data on the sex and size of the animal, and for some we have additional behavioural data. Using a set of microsatellite markers optimised for this species, you will test for large-scale genetic structure across the atoll, as well for small-scale structure within each island. On an individual level, you will test for associations between heterozygosity and size, and attempt to infer family relationships among individuals.

Using a unique collection of samples for a fascinating species, this project will provide you with valuable experience with DNA extraction, PCR and fragment analysis, as well as with an excellent introduction into the field of population and conservation genetics. Please note that this project does not involve fieldwork.
Contact: Dr. Erik Postma    last update: 2014-10-30

 

Habitat segregation between an allopolyploid plant and its parents - integrating manipulative experiment and next generation sequencing

Whole genome duplication between species (allopolyploidisation) occurs commonly in plants, but little is known about the molecular mechanism of adaptive significance of the originated species (allopolyploids). If an allopolyploid and its parent species have adapted to different environmental conditions, their fitness should be reduced outside the range of the current habitat. The allopolyploid may make use of genes inherited from either of the parents, depending on the environment. The project aims to determine whether environmental factors that vary among habitats in field cause difference in fitness in an allopolyploid plant and its parent scpecies, and how it is related to gene expression of the allopolyploid. Your work involves a manipulative experiment in a growth chamber and transcriptomic analyses using next generation sequencing (NGS), the latest genome sequencing technique.
Contact: Prof. Dr. Kentaro Shimizu  Dr. Rie Shimizu-Inatsugi Dr. Reiko Akiyama   last update: 2014-09-24

 

Variation in reproductive traits of old and new allopolyploid plants

An allotetraploid plant possesses two sets of genomes derived from two different parent species. Newly occurred allopolyploid may experience genomic changes e.g., chromosome rearrangements, which can lead to variation in phenotypic traits. Such variation may decrease over time as the population undergoes cell divisions and/or selection. Traits particularly relevant to this phenomenon should include those associated with reproductive success. An allotetraploid plant Arabidopsis kamchatica originated from A. lyrata and A. halleri ca. 105-106 years ago and today occurs in a wide range of habitat in Japan, from mountains to lowlands. In addition to such natural populations, there exist first few generations of synthetic A. kamchatica. The goal is to examine temporal fluctuation in phenotypes by quantifying the extent of variation in reproductive traits in A. kamchatica with old and new origin. The project may potentially develop into exploration of genes underlying traits with phenotypic variation.
Contact: Prof. Dr. Kentaro Shimizu  Dr. Rie Shimizu-Inatsugi Dr. Reiko Akiyama   last update: 2014-09-24

 

Growth of a recently occurred polyploid plant and its parent species

Rapid growth may be crucial at the early stage of colonization, especially if a species can only clonally propagate and is in competitive environment. The Swiss valley of Urnerboden saw a recent polyploydization event that a triploid Cardamine insueta occurred from C. amara and C. rivularis. The three species admix in an area that stretches several km along the valley. Using materials collected from field, you will conduct a chamber experiment to examine whether C. insueta surpasses the parent species in growth and whether growth varies depending on abiotic environmental conditions. Environmental parameters of the material collection points might possibly be incorporated from geographical survey data. The geographical part will be developed in collaboration with the Remote Sensing Laboratory of the University of Zurich.
Contact: Prof. Dr. Kentaro Shimizu  Dr. Rie Shimizu-Inatsugi Dr. Reiko Akiyama   last update: 2014-09-24

 

Do female-sterile ‘males’ contribute to sexual reproduction in the androdioecious species, Cardamine amara

In manual pollination trials in the lab, and in the field, female-sterile males are able to fertilise hermaphrodites, and produce viable seeds. What is currently not clear however, is to what extent this is happening in the field via normal (i.e. non-manual) pollination methods. Answering this question, would provide further compelling evidence that C. amara is indeed functioning as an androdioecious species, and give valuable insight into how female-sterile males can be maintained within a typically hermaphroditic population. This project would involve performing pollination assays in the common garden, and tracking parental genotypes through into the offspring generation. It may also be possible to perform pollen competition experiments.
Contact: Dr. Andrew Tedder  Prof. Dr. Kentaro Shimizu   last update: 2014-09-24

 

Evolution after gene duplication

Gene duplication is a frequent and important event during evolution. What happens when a gene that has two traits gets duplicated? Will the two copies stay multifunctional, specialise for the same function or subfunctionalise for different functions? Many theories and models have been proposed to understand the outcome of gene duplication, but little experimental data exist to address these questions. In this project you will address these questions with a laboratory evolution experiment using E.coli..
Contact: Dr. Yolanda Schaerli  Email:   last update: 2014-09-11

 

Adaptation to cold in ticks across altitudinal gradients in the Swiss Alps

As a consequence of their broad host range and their wide distribution, tick vectors have for a long time been considered as generalist parasites adapted to a large array of conditions. Alternatively, tick populations may consist of locally adapted populations that specialise in different habitats or host species. Climatic conditions, more than the distribution of potential hosts, are generally invoked to explain the range of ticks. A general shift of tick populations toward higher altitudes is observed in Europe and particularly in Switzerland. This shift could be due to a shift of the hosts, more favourable conditions or adaptation to new environments. You will investigate the genetic diversity of the NADH dehydrogenase gene, a mitochondrial gene involved in cold tolerance, along an altitudinal gradient in two sympatric tick species, one native at high altitudes and one currently colonising higher altitudes. You will help to collect ticks along altitudinal gradients in the Swiss Alps. Back in the lab, you will develop lab protocols to sequence mitochondrial genes. Finally you will learn how to quantify altitudinal clines and to compare them between tick species.
Contact: Dr. Mélissa Lemoine  Prof. Dr. Barbara Tschirren   last update: 2014-05-14

 

Parasite-mediated selection on candidate immune genes along altitudinal gradients in the Swiss Alps

Understanding why individual hosts as well as host populations differ in their resistance to parasites, and how this affects the evolution of parasite virulence and host life history are fundamental quests in the field of evolutionary ecology. At the same time, it can provide an evolutionary framework for the applied management of human and wildlife diseases. In this project you will study patterns of parasite-mediated selection acting on candidate genes for parasite-resistance in free-living rodents along an altitudinal gradient in the Swiss Alps. During this project, you will help to catch rodents along altitudinal gradients. Back in the lab, you will use molecular methods to genotype rodents for candidate genes as well as neutral genetic markers. Using statistical methods, you will learn how to detect selection acting on genes, if this selection differs along altitudinal gradients, and if patterns of selection differ between immune genes and neutral markers.
Contact: Dr. Mélissa Lemoine  Prof. Dr. Barbara Tschirren   last update: 2014-05-14

 

The transmission of non-genetic effects across generations in Japanese quail

Mothers can transfer non-genetic information to their offspring and thereby influence the development and behaviour of their young. Such maternal effects can help offspring to deal with environmental conditions encountered early in life and they have been suggested to accelerate adaptation to environmental change. In this project you will test in a captive population of Japanese quail how information is transferred across generations and how genetic and non-genetic maternal effects influence reproductive decisions of daughters and grand-daughters. Birds offer some clear advantages for the quantification of the role of prenatal maternal effects in shaping the daughters’ maternal investment because the embryonic development takes place outside of the mother’s body and prenatal maternal resource investment (i.e. egg composition) can easily be manipulated. You will directly manipulate egg composition and test for consequences of maternal investment on behaviour, morphology and reproductive investment in daughters and grand-daughters (quails have a generation time of 6 weeks!). Furthermore, the project will allow you to perform ecophysiological measurements. This project is ideal for a student who is interested in evolutionary biology, animal behaviour and eco-physiology, and would like to spend a substantial amount of time doing practical work with quails.
Contact: Prof. Dr. Barbara Tschirren    last update: 2014-05-14

 

Rapid evolution and population dynamics in an alpine rodent, the snow vole

Studying contemporary evolution in the wild is instrumental to explaining the origin of biodiversity. At the same time, it helps understanding and predicting the consequences of the anthropogenic changes challenging wild populations worldwide. Currently our ability to understand and predict the evolutionary dynamic of natural populations is limited by a lack of integration of the different aspects of their biology. In this project you will combine information on, among others, demography, genetics and selection to get a better insight into how evolutionary and ecological phenomena influence each other, and how they shape a population.
For eight years, we have monitored a snow vole population near Chur. This population lives in a harsh and variable environment, which imposes contrasting selection pressures and results in large fluctuations in population size across time. Thereby it provides an fantastic opportunity to disentangle the links between evolution and ecology in the wild.
We have an extensive data set including a complete pedigree of the population, genetic data, morphological and life history data, demographic rates, dispersal, temperatures, snow cover etc., and we can extend this list if you would like to measure other traits.
Contact: Timothée Bonnet  Dr. Erik Postma Research Group page   last update: 2014-02-28

 

Human life-history evolution: An evolutionary investigation into life as we know it

Humans are complex animals, and being humans ourselves, we are particular aware of this. At the same time however, we have a level of insight into these complexities that is unattainable when looking at other species than ourselves. Furthermore, it is this complexity, arising from our extensive culture and ability to shape our environment, that make our species a particularly fascinating object of study.

Using a unique genealogical dataset, you will investigate the proximate and ultimate causes and consequences of variation in key human life-history traits, like family size, lifespan and age at first reproduction.
Integrating evolutionary biology, anthropology and history, this project will provide a unique insight into our evolutionary past, present and future.
Contact: Dr. Erik Postma  Research Group page    last update: 2014-01-09

 

Evolutionary history of human parasites

The recent Human Microbiome Project is revealing that our bodies play host to hundreds--if not thousands--of different species in our guts and scalps that may be carrying out beneficial (and not just detrimental) functions to ourselves and our ecosystems. While scholars such as Jared Diamond have explored the role that germs have played in human history, there has been little attention to the role of larger parasites in human affairs, from physiology and behaviour to migration and social interaction. This project will endeavor to produce a cultural history of a key parasite (such as lice, Guinea worms, pinworms, eyelash mites). Questions asked include:

  • How have parasites changed human lifestyles?
  • How have the possible benefits of parasites been utilized by the medical profession, as in the treatment of allergies?
  • Are humans and human activities (through the Gaia Hypothesis) integral to endosymbiotic processes like those forwarded by Lynn Margulis?

Contact: PD Dr. Marc Hall    last update: 2014-10-24

 

Natural selection at the center and edge of the distribution

The boundaries of geographic distributions present a puzzle: why do species not simply evolve the ability to extend their ranges? One set of hypotheses involves natural selection becoming either more severe at distribution edges, or more distinct from selection at the center of the range. These hypotheses have not yet been tested.
You will perform a field experiment on the Common Frog (Rana temporaria) to measure selection acting on individual tadpoles across an elevational gradient from the valley floor to the upper edge of the distribution at 2500 m in the Alps. The question is, how does the "adaptive landscape" shift across the gradient? The project involves experiments in mesocosms and natural ponds, measurements of tadpole morphology and behavior, and an emphasis on statistical estimation of selection.
Contact: PD Dr. Josh Van Buskirk    last update: 2012-09-26

 

Sequencing pollen S-genes in Solanum chilense

The species S. chilense (a wild relative of tomato) uses RNAses to degrade pollen tubes to prevent self-fertilization. RNAses comprise the female side of the recognition reaction, but using next‐generation sequencing, we will attempt to identify the male, pollen genes also responsible for "self"‐incompatible genetic interactions. This will involve phenotyping and evolutionary genetic analyses of these genes. The molecular basis of this mechanism is highly dynamic and genetically different than other known SI systems, where evolution for self‐ recognition resembles disease resistance and pathogen detoxification mechanisms.
Contact: Dr. Tim Paape  Prof. Dr. Kentaro K. Shimizu   last update: 2012-09-26

 

Size- and nutrient dependent time-budgets and pairing success of yellow dung fly (Scathphoaga stercoraria) males in the field

Animals have to trade off their daily time and their energy reserves between foraging and mating activities. This trade-off likely depends on body size. Yellow dung fly males spend most of their time around dung pats waiting for females to mate with, as this is how they can best maximize their reproductive success. However, individuals have to forage some time for nectar (their energy source) and prey (their source of protein), for which they have to leave the pasture. Small males lose in direct mate competition against larger males, but they could increase their mating success by spending more time at the mating site. The latter is possible if small males need less food and/or if they spend less energy per unit time or body mass. By marking and tracking field males that have been fed different diets, this project assesses the size-dependent time (and energy) budgets of yellow dung flies to find possible physiological advantages of small body size.
Contact: Prof. Dr. Wolf Blanckenhorn  

 

Temperature sensitivity in latitudinal yellow dung fly populations

The response of animals to thermal extremes may be associated with fitness benefits or costs resulting e.g. from an increase in the expression of stress proteins such as heat shock proteins HSP. We investigate systematic variation in thermal tolerance and fitness-related traits in the yellow dung fly across a latitudinal gradient ranging from Sweden to Spain by measuring temperature- and size-dependent reproductive success of females and males under semi-natural conditions in the laboratory.
Contact: Prof. Dr. Wolf Blanckenhorn  

 

Comparative reproductive behaviour, life history and morphology of sepsid flies (Diptera: Sepsidae)

Males have a limited amount of resources to invest in reproduction. This suggests a rich evolutionary interplay between traits that enhance mating success and those enhancing fertilization success, the outcome of which is expected to vary strongly with the mating system. By using phylogenetic, population genetic and experimental approaches, we investigate in an integrative manner how mechanisms of pre- and post-copulatory sexual selection interact and contribute to the divergence in sexual size dimorphism, genital and secondary sexual trait morphology, and mating behavior among species and populations of Sepsid flies (Diptera: Sepsidae). Three related projects can be offered.

  1. A first project targets the role of pre- and post-mating sexual selection acting on various genital and body traits in several closely related sepsid species.
  2. A second, common garden project addresses the phenotypic plasticity and heritability and hence the evolvability of the studied traits and their scaling relationships in the same species.
  3. A third project is a population genetic/genomic approach that compares quantitative genetic variation relative to that of neutral genetic markers using multiple populations of two species showing contrasting patterns of sexual size dimorphism.
  4. A fourth project employs quantitative trait locus (QTL) mapping of key behavioural, physiological and morphological traits in possibly hybridising, closely related and sympatrically occurring species to identify key candidate genes affecting natural and sexual selection.
  5. A fifth project involves genome-wide association studies (GWAS) of ecologically relevant behavioural, physiological and morphological traits by comparing latitudinal populations of various widespread sepsid fly species in Europe, Asia and North America.

Contact: Prof. Dr. Wolf Blanckenhorn  Dr. Martin Schäfer

 

The role of surface pheromones for sexual selection in Sepsid flies

Sepsid flies show a high diversity in body sizes, sexual size dimorphism, mating system and mating behavior. Sexual selection on body size obviously contributes to the evolution of body size and dimorphism, but will highly depend on the mating system. We study sexual and fecundity selection on body size in various sepsid species. However, behavioral traits such as courtship or short-distance and surface pheromones likely play an equally important role for male mating success as body size. We investigate the role of surface proteins (phereomones) in sexual selection in various sepsid species using gas chromatography and mass spectroscopy (in collaboration with Dr. Florian Schiestl, Institute of Systematic Botany).
Contact: Prof. Dr. Wolf Blanckenhorn
Florian Schiestl, Institute of Systematic Botany