Potential thesis topics

Are you looking for a project for your Bachelor or Master thesis? We are always happy to welcome new team members! Below you can find an overview of the currently available projects per research topic and the corresponding contact person.

Please note: the descriptions are outlines and represent possible directions of the projects during the next two years (2021-2023). The final direction of your project depends on your input and ideas, as well as on available funding and data sources.

Get in touch if you are interested!

​​1. Evolutionary ecology of two coexisting stickleback species

​Contact person: Thijs Mattheus Peter Bal; Collaborators: Konstantinos Sagonas, Joost Raeymaekers

Studying the mechanisms behind population divergence and local adaptation is a large aspect of modern evolutionary biology. Increasing our understanding of these concepts is important for conservation ecology and landscape management. It is for instance an important question which evolutionary trajectories different species may take when they experience environmental change. One approach to answer this question is to use natural populations and study how variation is distributed in the system in relation to the landscape.

In our research we use ecologically similar and coexisting three-spined and nine-spined stickleback fishes as models for understanding evolutionary change in a natural system. These two species co-occur in the riverine landscape of Belgium and the Netherlands and this system encompasses significant environmental differences on a relatively small geographical scale. We use a broad approach and we utilize different types of data to study the (adaptive) variation between individuals, populations and species.

Topic 1A: The role of genomic structural variants in local adaptation

Single‐nucleotide polymorphisms (SNPs) are one of the most widely used types of genetic variation for studying signatures of local adaptation, but in recent years there has been an increasing interest in the role of structural variants. The main goal of this thesis topic is to identify genomic structural variants that potentially play a role in local adaptation in coexisting three-spined and nine-spined stickleback. Earlier research within this study system using SNPs has revealed stronger signatures of selection in three-spined stickleback than in nine-spined stickleback. However, it is still largely unknown how much structural variants contribute to the level of genetic variation, and more importantly, the role they play in local adaptation in the two species. It is for example possible that three-spined stickleback again show stronger signatures of selection than nine-spined stickleback when looking at this type of genetic variation, strengthening the hypothesis that three-spined stickleback overall have a stronger evolutionary response. Another interesting possibility is that nine-spined stickleback actually show stronger signatures of selection for this type of genetic variation, revealing that selection simply has the potential to leave different genomic signatures of adaptation in species experiencing similar selection pressures. Indeed, all possible findings have major implications for understanding local adaptation in this system and hence it is highly important that the role of genomic structural variants is assessed.

In this project the student gets access to whole genome sequences of 192 individuals of each species. This project is suited for students with a strong interest in (population) genomics and (learning) bioinformatics. There is a lot of data available and different approaches as well as different specific research questions can be explored. For this reason, personal input and creativity by the student is also encouraged. The student will closely collaborate with Thijs and has the chance to be involved in the writing of a manuscript aimed for publication in a peer-reviewed scientific journal.

2. Population genomics of Lake Tanganyika sardines

Contact person: Leona Milec; Collaborators: Joost Raeymaekers and Els De Keyzer

In this project, we focus on two sardine-like freshwater fishes, Limnothrissa miodon and Stolothrissa tanganicae, which feed millions of people in Central and West Africa. We generate genomic resources, investigate their population structure, local adaptation, and resilience to climate change and fishing pressure. The results will be used to inform fisheries management and aid the development of sustainable management practices. Click here for more info about the project.

Topic 2A: Adaptation to new lake environments following introduction/invasion – the case of L. miodon

The freshwater sardine L. miodon, originally endemic to Lake Tanganyika, has been introduced into several smaller lakes in the surrounding countries for fishery purposes, including the natural Lake Kivu and the man-made reservoirs Kariba and Cahora Bassa. Using RAD-tag sequencing data and a combination of population genomic and demographic modelling approaches, we aim to address how the sudden exposure of L. miodon to its new and distinct environments may have influenced its life history, genetic diversity and population differentiation. Knowledge of phenotypic and genetic changes following introduction will prove instrumental to meet the unique management needs of each lake. The student will closely collaborate with Leona to participate in laboratory work, and genetic and bioinformatic analyses.

Topic 2B: Population genetic structure of L. miodon in relation to spawning grounds

The population dynamics of fish are often strongly coupled to their spawning and nursing grounds. Both climate change and fishing pressure in and around these areas are likely to induce changes in the distribution of these grounds and recruitment success, in turn influencing population structure of the fish. Juveniles of the semi-littoral clupeid L. miodon are heavily harvested in Lake Tanganyika, yet its spawning behaviour has barely been studied. We use COI barcoding to verify the species identity and link the population structure of juveniles and adults of L. miodon along the North-South axis of Lake Tanganyika, to infer spawning migration and loyalty to nursing grounds. The student will closely collaborate with Leona to participate in field work, laboratory work, and genetic and bioinformatic analyses.

Topic 2C: Historical versus contemporary population genetic structure of Lake Tanganyika sardines

Over time, increased fishing pressure in Lake Tanganyika might have affected the resilience of our two sardine species Limnothrissa miodon and Stolothrissa tanganica. In addition, climate changes has changed the Lake Tanganyika environment in ways which could have influenced the biology of the two species as well. In this study, we will compare the contemporary population genetic structure of the Lake Tanganyika sardines with their historical population genetic structure. For this we will make use of samples collected in 2016-2018 on the one hand, and samples from the 1990s on the other hand. For both time windows, samples are available for the North, centre and South of the lake, and so we will be able to test if the lake-wide population structure changed in the course of almost 30 years. Because the samples from the 1990s are older and have not been preserved optimally, the DNA is quite degraded. This implies that we have to rely on specialised lab work to extract the DNA. In addition, we will use a DNA capture technique to target specific genomic regions. This will facilitate the sequencing of the historical DNA which is expected to be more fragmented. Bioinformatic analyses will also be required to optimize the DNA capture approach. The project will be organised in collaboration with the University of Leuven in Belgium.

3. Parallel evolution in a marine snail

​Contact person: Anja Westram; Collaborators: Joost Raeymaekers

How do organisms adapt to their local environment? This question is a main focus of evolutionary biology. It becomes especially urgent in times of anthropogenic climate change. The marine snail Littorina saxatilis is an ideal system to study adaptation to spatial temperature gradients on both large and small geographical scales, and in the group we are interested in how adaptation works at both the phenotypic and the genomic level.

Topic 3A: Physiological measures of temperature adaptation

In this project, we will focus on small spatial scales, sampling intertidal cliffs on the coast around Bodø. Individual cliffs are associated with a temperature gradient because the upper part of the cliff is submerged for shorter amounts of time and thus experiences higher temperatures in summer. We will ask whether snails sampled from the upper part of the cliff are more resistant to desiccation and show physiological adaptation to heat, while snails sampled from the lower parts of the cliff are less well adapted to heat. For this, we will develop physiological assays, based on the literature as well as our own ideas. We will then apply these assays to large numbers of snails from different parts of the cliff and test for significant differences. The student will learn about main evolutionary processes, experimental design and statistical analyses. Creativity and interest in developing practical setups are required, as well as a motivation to do fieldwork. The student will closely collaborate with the newly-starting Littorina team; the results of the project will be very useful for our large study on the genomic basis of temperature adaptation in snails.

Topic 3B: Testing for parallel temperature adaptation in sister species

L. saxatilis co-occurs with a sister species, L. arcana. It will therefore be interesting to test whether similar patterns of local temperature adaptation can be found in both species, indicating “parallel evolution”, where different populations or species evolve similarly in response to similar selection pressures. In this project, we will thus apply assays developed under topic 3A to individuals sampled from shores where both species occur, and then compare temperature response between different parts of the cliff and between species. As L. saxatilis and L. arcana are difficult to distinguish morphologically, this project will involve analysing genetic markers that show differences between the two species and can thus be used for species identification. This project will be interesting for someone who is keen to learn about evolutionary processes and would like to get insights into various methods used in evolutionary biology, including fieldwork, experiments, and simple genetic analyses.

4. Genetic and non-genetic adaptation in stickleback fishes to natural and human-impacted environments

Contact person: Brijesh Yadav/Aruna M Shankregowda; Collaborators:  Joost Raeymaekers and Deepti Patel

Human-induced pollution features among the greatest challenges that organisms face for survival and adaptation. Aquatic ecosystems are exposed worldwide to varying degrees of pollution. The fitness of their communities and populations has been affected to such an extent that biodiversity is compromised. The adaptive capacity of stickleback fishes, from their cells to their overall performance, allows them to adjust to environmental change. Through a set of experiments on wild and lab-reared sticklebacks, we aim to understand their adaptive responses to aquatic conditions at three levels: responses to combined mercury and temperature stress (topic 4A), adaptation to salinity (topic 4B), and through interactions with the gut microbiome (topic 4C). These subjects will give you an understanding of how organisms adjust to new environmental conditions (through physiological responses or interaction with the microbiome) or adapt to their environment (through evolutionary change). Indeed, assessing the link between responses from cellular to organismal levels, using a diversity of fitness indicators and behaviour, provides a fundamental understanding of how organisms as a whole may adjust to prevailing in a future world.

The student will closely collaborate with Arun and Brijesh to participate in field sampling, laboratory work, and genetic and bioinformatic analyses.

Topic 4A: Biological responses of three-spined stickleback to mercury and temperature stress

Mercury (Hg) is one of the most toxic and wide-spread pollutants in aquatic environments. It bio-accumulates as methylmercury (MeHg) in organisms and biomagnifies in the food chain. The rapidly changing climate may enhance these harmful effects because higher temperatures may increase Hg methylation rates. This risk is particularly high in high latitude populations, as those are expected to undergo the most severe temperature changes. We investigate the combined effect of temperature stress and exposure to Hg and use RNA-sequencing to identify differentially expressed genes, proteins, and pathway enrichment. We will use experimental populations as well as populations from pristine and Hg polluted sites. The experimental part will also include the study of Hg accumulation, survival, growth, body condition, and behaviour.

Topic 4B: Local adaptation along an environmental gradient in the three-spined and nine-spined stickleback:

Salinity gradients are a challenging feature in the environment of many aquatic organisms because there are many obstacles to achieve the transition from marine to freshwater habitat. The most physiologically demanding challenge is the salt concentration in the water. Many of these habitat transitions might lead to adaptive evolution or speciation. The characterization of transcriptomic differences between populations from marine and freshwater environments is important to better understand this process, as gene expression patterns can evolve rapidly. Stickleback fishes have repeatedly transitioned from marine to freshwater habitats and are thus great study models to understand this important ecological barrier. The first task in this project will include sampling various populations of the three-spined and nine-spined stickleback from brackish and freshwater habitats. RNA transcriptome experiments will then be conducted to test for differential gene, protein, and biological pathway expression among these populations.

Topic 4C: Role of gut microbiome composition during local adaptation in stickleback

Many marine stickleback populations independently colonized and adapted to freshwater environments at the end of the last ice age, about 11,000 years ago. This process of parallel adaptation to freshwater is characterized by genetic, morphological, and physiological changes. Both three-spined and nine-spined stickleback are excellent study species for revealing the relationship between host local adaptation and gut microbial communities in nature. The gut microbiota co-evolve with their host and play a crucial role in the host’s functioning of various biological processes. It also represents a critical element in establishing new ecological niches. In this project, we aim to examine differences in gut microbial community composition between brackish water and freshwater populations of both stickleback species.

5. Diversity of micro-organisms in Northern Norway

Contact person: Lynn Govaert; Collaborators:  Joost Raeymaekers

Are you fascinated by small ponds and lakes? Did you ever wonder what microscopic life these freshwaters harbour? If yes, then we might have a thesis topic for you! In my group, we investigate species and genetic diversity of micro-organisms with a particular focus on protist species. Protista is a very broad group, ranging from algae to protozoan and slime molds. In this project, we focus on protozoan. You will combine fieldwork with laboratory experiments and survey protozoan communities of natural freshwater ponds along an latitudinal gradient in Norway. In particular, you will identify the different species found via metabarcoding and microscopy. This project will highly contribute to the largely unknown micro-organismal diversity harboured in freshwater ponds in Northern Norway. Do not hesitate to contact me with further questions or if you want to know more about what my group is doing, please check my webpage here or here.