Landscape Genomics Group

​​1. Evolutionary ecology of two coexisting stickleback species

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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 about 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 1: Genomic architecture and the propensity for adaptation

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The main goal of this thesis topic is to identify the genomic regions that play an important role in local adaptation in coexisting three-spined and nine-spined stickleback. Earlier research within our study system has shown that three-spined stickleback possibly have a stronger evolutionary response to environmental pressures than nine-spined stickleback. The genomes of the two species are similar in size, however, structural variation in genomic architecture (linkage blocks, inversion polymorphisms, copy number variations...) might underlie differences in the propensity for adaptation. In this project the student will assess the whole genome sequences of 192 individuals of each species to test this hypothesis.

 

This project is suited for master 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.

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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 2020/2021 to DR Congo, Zimbabwe, Mozambique, or Zambia to collect samples of S. tanganicae and L. miodon for RAD-tag sequencing, and morphological and life history characterization (e.g. number of gill rakers, size at maturity).

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Topic 1: 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 field work, laboratory work, and genetic and bioinformatic analyses.

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Topic 2: 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 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.

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Topic 3: 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 tanganicae. 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 in samples from the 1990s on the other hand. For both time windows, samples are available for the North, center 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 much older and have not been preserved optimally, the DNA is quite degraded. This implies that we have to rely on specialized 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 organized in collaboration with the University of Leuven in Belgium.

3. Parallel evolution in a marine snail

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Contact person: Anja Westram

Collaborators: Joost Raeymaekers

 

Parallel evolution happens when similar phenotypes evolve in multiple geographical locations, in response to similar selection pressures. Taxa showing extensive parallel evolution are very useful to understand the genetic basis of local adaptation and the repeatability of evolutionary processes. The marine snail Littorina saxatilis provides an example of such a taxon, with divergent ecotypes that repeatedly evolved in many locations across Europe. A thick-shelled, wary ecotype lives in areas of the shore where predatory crabs occur, whereas crab-free parts of the shore contain a thin-shelled, bold ecotype. However, it has never been formally tested whether crabs drive the repeated evolution of the thick-shelled ecotype. Moreover, it is unclear whether the genetic variation leading to repeated evolution of this ecotype is segregating as standing genetic variation throughout the distribution range of L. saxatilis, enabling rapid adaptation when crabs expand their range. The coast around Bodø is ideal to answer these questions as it is close to the northern range limit of the main predatory crab species, allowing for a comparison between crab-inhabited and crab-free areas. We will test 1) whether divergent ecotypes exist in Norway, using morphological and genetic analyses, and asking whether the thick-shelled ecotype is restricted to the southern areas where crabs exist; and 2) whether the genetic variants (particularly chromosomal inversions) required for ecotype divergence exist in the northern areas where predatory crabs are absent. The student will closely collaborate with Anja and Joost to participate in field work, laboratory work, and genetic and bioinformatic analyses.

4. Gene flow in the Deep: are fjord populations of benthic amphipods connected via tidal currents?

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Contact person: Joost Raeymaekers

Collaborators: Henning Reiss, Truls Moum and Pascal Hablützel

 

Oceans and fjords are well-connected ecosystems allowing for many opportunities to disperse. However, benthic organisms living in the deep sea and deep in the fjords might be strongly isolated because of the patchiness of their habitat, their narrow ecological niche, or a generally weak dispersal capacity. In this thesis project, we aim to investigate the degree of population connectivity in Lysianassidae. Lysianassidae are a family of amphipods, an order of mostly detritivorous or scavenging crustaceans. They occur in enormous densities, and may therefore play a key role in the nutrient recycling of the fjord ecosystem. In the fjords of Northern Norway, Lysianassidae are found at 10 to 1000 meter depth. These deep zones are separated by shallow underwater barriers, possibly substantially limiting dispersal of amphipods (and other deep water specialists). As a consequence, amphipod populations become genetically isolated, allowing strong local adaptation and high genetic diversity at the landscape scale. The planned work includes sampling a number of different fjord systems, starting with Saltenfjorden and Skjerstadfjorden near Bodø. Both fjords are connected by Saltstraumen, the world's strongest tidal current. Samples will be obtained at various locations in both fjords using baited traps. Afterwards, amphipods will be sorted, and the species will be identified using diagnostic morphological traits. Then DNA will be extracted, and genetic data will be obtained by DNA sequencing and bioinformatic analyses. Specifically, the species status will be verified using barcoding with the COI gene, and gene flow between the different fjord populations will be calculated using SNPs to infer the degree of population connectivity within and between fjords. The master student is expected to participate in fieldwork, and to perform the morphological, genetic and bioinformatic analyses. This Master thesis could be coupled to a second thesis about the ecological role of scavenging amphipods, their depth zonation and response to fish farming in sub-Arctic fjords.

5. Genetic and non-genetic adaptation in stickleback fishes

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Contact person: Aruna M Shankregowda

Collaborators: Konstantinos Sagonas, Joost Raeymaekers

 

The capacity of species to respond to environmental changes largely depends on their evolutionary potential, which is rooted in the amount and structure of adaptive genetic variation. However, species may compensate for low evolutionary potential through phenotypic or behavioural plasticity (non-genetic mechanisms). Adaptive plastic responses to natural selection may be modulated by the regulation of gene expression, for instance via epigenetic modifiers such as DNA methylation. Yet, intestinal microbiota, assisting in various important biological functions, may act as another, entirely different key element underlying the establishment of new ecological niches. The current project aims to improve our understanding on how adaptation is achieved in natural populations beyond the genetic level. Specifically, we aim to determine the role of both epigenetic mechanisms and microbiota in local adaptation in two coexisting and closely related fishes, the three-spined and nine-spined stickleback. We will 1) quantify the relative importance of epigenetic vs. genetic mechanisms for local adaptation (using a next-generation sequencing approach RRBS); 2) determine the contribution of regulatory mechanisms (miRNA regulation on genes subject to natural selection) to local adaptation; and 3) determine the role of gut microbiome  (intestinal bacterial diversity based on 16S ribosomal RNA (rRNA) gene amplicons) in local adaptation. The student will closely collaborate with Arun to participate in laboratory work and to perform the genetic and bioinformatic analyses.