Bachelor and Master thesis projects

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 (2019-2020). The final direction of your project depends on your input and ideas, as well as on available funding and data sources.

1. Evolutionary ecology of coexisting stickleback species

Contact person: Thijs Mattheus Peter Bal

Understanding the mechanisms underlying population divergence and local adaptation are a major focus in current evolutionary biology. Increasing the knowledge about these concepts is of importance for conservation ecology and landscape management. It is for instance an important question which evolutionary trajectories different species can take when experiencing environmental change. In our research we use phylogenetically related and coexisting three-spined and nine-spined stickleback as models for studying drivers of evolutionary change and how this is related to species-specific properties. We study this in a natural riverscape system that encompasses considerable variation in local environmental conditions. In our research we take a broad approach using different types of data to study the variation between individuals, populations and species.

 

Large amounts of data and materials are already available for the research projects. Yet, under this research topic students have the possibility to join a fieldwork campaign to collect new stickleback in spring 2020 (March/April) to the Netherlands and Belgium. The duration of this campaign is about a month. Availability to join during this field campaign is not a necessity for participating in one of the research projects.

Project 1 (Msc): Genomic architecture and the propensity for adaptation

The goal of this project is to identify the genomic regions and architecture underlying adaptation and divergence using resequenced  stickleback genomes. Potential important genomic architecture differences have previously been identified in the form of linkage blocks, inversion polymorphisms and copy number variations and these could be used as starting points. This project is suited for students with interests in bioinformatics and genomics.

Project 2 (Bsc/Msc): Morphological variation and ecological divergence

The goal of this project is to study morphological variation, an important indicator of ecological divergence. To do this, the student will use photographs of sticklebacks and software for body measurements and geometric morphometrics. The project can be expended by including the analysis of stable isotope data, which is used to infer the trophic position of individuals. This project is suited for students with interest in ecology.

Project 3 (BSc/Msc): Sequencing output filtering and the effect on downstream analyses

The goal of this project is to determine what effect variational filtering parameters applied to raw sequencing output have on the downstream analyses. Before the statistical analyses that test ecological and evolutionary hypotheses are performed, the raw sequencing output usually first gets processed and filtered. Filtering decisions made during this early phase could potentially influence the outcome of downstream analyses and subsequently the biological interpretation. This project is suited for students with interests in bioinformatics and statistics.

Project 4 (MSc): Library preparation methods and the effect on downstream analyses

The goal of this project is to test to what extent DNA library preparation methods could affect the sequencing output and subsequently the genomic analyses. The choice of a specific library preparation protocol could affect the sequencing output and in that way affect the results of a study. The student will use whole-genome resequencing data output of the same stickleback, but generated using different library preparation protocols to test whether there are differences in downstream analyses results. This project is suited for students with strong interests in molecular laboratory techniques, bioinformatics and statistics.
(Continuation of this project is dependent on collaborators at the Norwegian Sequencing Centre and not 100% assured)

2. Population genomics of Lake Tanganyika sardines

Contact person: Leona Milec

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.

Students may have the opportunity to participate in a capacity-building workshop (have a look at our blog to see how this usually looks like) and field campaign in 2020 to DR Congo, Zimbabwe, Mozambique, and/or Zambia to collect samples of S. tanganicae and L. miodon for RAD-tag sequencing, and morphological and life history characterisation (e.g. number of gill rakers, size at maturity).

Project 1 (Msc): 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.

Project 2 (Bsc/Msc): 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 behavior has barely been studied. We use RAD-tag sequencing data to 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.

 

Project 3 (Bsc/Msc): Mitogenome of L. miodon and S. tanganicae

The mitochondrial genome of an organism can provide an important resource for phylogenetic and molecular evolutionary studies. We aim to extract the sequence of the mitochondrial genome of L. miodon and S. tanganicae from our recent draft assemblies, characterize and compare them using homology based approaches, and put them in the phylogenetic context of the Clupeiformes.

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