Research team

Systemic Physiological and Ecotoxicological Research (SPHERE)

Expertise

My main expertise is evolutionary genomic analysis of whole-genome sequencing data. I have been working on a variety of organisms including plants, monkeys and fishes. We also work with crosses and experimental setups in African cichlid fishes. One main focus of my work is the role of hybridisation and genetic exchange in diversification and adaptation. I also have a background in theoretical population genetic and ecological modelling using mathematical models and computer simulation.

Evolutionary paths to adaptive divergence: The role of ancient and ongoing hybridisation in rapid speciation of sailfin silverside fishes. 01/10/2021 - 30/09/2022

Abstract

Adaptive radiations are showcases of evolutionary processes, characterised by rapid diversification of one ancestral lineage into an array of closely related species. We still do not understand how speciation, normally a slow process, can occur in such fast bursts. Recent genome-wide molecular studies suggest that rapid diversification might be fueled by cross-species hybridisation. In this project, I will obtain an integrative picture of the effects of hybridisation on the creation and maintenance of diversity in an adaptive radiation. The sailfin silverside fishes in Lake Matano, Sulawesi, are a rare case of adaptive radiation showing indications of both historical and ongoing hybridisation with an ancestral riverine lineage. This makes sailfin silversides uniquely suited to investigate the interplay of hybridisation and speciation in situ. I will perform the first genome-wide characterisation of the sailfin silverside radiation. Using whole-genome sequencing and innovative statistical approaches, I will resolve evolutionary relationships within the radiation, address the role of historical and ongoing hybridisation during diversification, and identify links between genetic exchange and ecological divergence. By establishing a thorough genomic context for all species of the radiation I advance the silverside radiation as a new model system in evolutionary biology and drive the development of statistical approaches that will be beneficial for future evolutionary research.

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The role of chromosomal inversions in the rapid evolution of biodiversity. 01/01/2021 - 31/12/2024

Abstract

Understanding how biodiversity evolves is a defining question in evolutionary biology and instrumental in conservation and mitigation in the face of global change. Recent work, including ours, suggests that new combinations of old genetic variants are a driving force in rapid adaptive diversification. There is a large body of theory predicting that inversions – chromosomal rearrangements in which a segment of a chromosome is reversed end to end – play a decisive role in this process, for example, by linking together adapted alleles. There is strong evidence for the role of inversions in adaptation of natural species, but we are lacking a quantitative assessment of the role of inversions in diversification of a large group of related species. We will fill this gap by characterising the occurrence, evolution, and role of inversions across the fishes of the extraordinarily diverse Lake Malawi cichlid adaptive radiation. For this, we will combine innovative molecular and computational approaches with a unique set of hybrid crosses between species up to two million years divergent.

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The genomic and ecological basis of rapid change in a functionally significant trait: osteoderm evolution in a girdled lizard. 01/01/2021 - 31/12/2024

Abstract

Osteoderms are bony elements that are expressed in the skin of a few disparate groups of tetrapods (i.e. in crocodiles, turtles, armadillos, and some lizard and frog species) – but not in other taxa. In humans, osteoderms are frequent complications of injury and in a few rare inherited disorders. Osteoderms spark interest because they are ecologically relevant (they are likely to function in body protection, thermoregulation and water budget maintenance, in mineral storage) but at the same time exhibit an unusually binary distribution (i.e., they are expressed completely, or not at all). The latter element facilitates research into the genomic substrate of the trait. One species of cordylid lizard, Hemicordylus capensis, uniquely displays intraspecific variation in osteoderms: the trait has evolved repeatedly and therefore is present in some populations, but not in others. The species thus offers exceptional opportunities for learning how, why and when this remarkable trait evolves. With this project, we aim to resolve those issues through a thoroughly integrated approach combining state-of-the-art genomic, functional morphological and ecological techniques. We will also explore if we can extrapolate the findings on this study system to other taxa that (occasionally) express osteoderms, including humans. The project will allow a rare complete view of the evolution of an ecologically relevant phenotypic characteristic with a remarkably discontinuous variation and an unusually disparate taxonomic distribution.

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The biodiversity, biogeography and evolutionary history of the northern basins of the Great African Lakes : the enigmatic fish faunas of Lakes Kivu, Edward and Albert revisited (KEAFish). 15/12/2020 - 15/03/2025

Abstract

The area of the northern East African rift-valley lakes, Kivu, Edward and Albert (KEA) is one of the most enigmatic regions in terms of its biogeography. The region is situated at the intersection of three major ichthyo-geographic provinces (Nilo-Sudan, East Coast and Congo), features a turbulent tectonic history and likely acted as a species reservoir during recent climatic changes such as the major drought some 15.000 y BP, which resulted in a complete desiccation of Lake Victoria. We suggest to combine classical taxonomy with state-of-the-art genomic methods to provide a comprehensive characterisation of the heavily understudied fish fauna of this region. This work will provide key insights into the regions' bio-geographic history, evaluate its role as a species refuge, and test its previously suggested role as the origin of the about 600 species of the Lake Victoria haplochomine cichlid radiation. Our research hypothesis is that an out-of-Kivu origin for cichlids and non-cichlids and the role of refuges of the KEA lakes shaped to a large extent the ichthyo-diversity of the region. While well-studied in temperate regions, the role of refuges in tropical freshwater fishes remained largely overlooked, which makes this study challenging and innovative. We will perform a region-wide COI-scan of the non-haplochromines of the region and complement with additional nuclear markers when necessary. We will then solve the taxonomic issues revealed, to create the necessary solid base to forward evolutionary and biogeographic scenarios. Two genera are already earmarked for morphometric revisions, the small cyprinids of the genus Enteromius and the catfish genus Amphilius. Because of the uninformative nature of the results of standard sequencing techniques in haplochromines, we will concentrate on RAD-sequencing for this group. We will complement samples from the region to an ongoing small-scale project that is concentrated on Lake Edward, to the mutual benefit of both projects. For this, the samples need to be properly identified. Major obstacle here is the lack of knowledge of the Lake Albert assemblage. Hence, a morphometric revision is included. We will also use RAD-sequencing for selected non-haplochromines in order to acquire the necessary detail to finetune the evolutionary and ichthyo-geographic scenarios. These include the species-rich genus Enteromius and the widespread cichlid, Oreochromis niloticus, and catfish Clarias gariepinus. For the latter, unpublished data indicate also an out-of-Kivu scenario. All analyses can be executed based on material collected during the HIPE-project, but one expedition to the Kivu area is planned to collect complement the samples for genetic studies. If necessary, DNA will be extracted from preserved collection specimens. As outputs, we envisage a database of genetic barcodes and RAD sequences for the fishes of the region, revisions of key fish groups (haplochromines and others), phylogeographics and evolutionary history reconstruction for several important fish groups, and formulation of a scenario for the ichthyo-geography of the KEA region.

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The use of alternative genomic markers to reconstruct the complex evolutionary histroy of neotropical small felids. 01/11/2020 - 31/10/2022

Abstract

Tracing the evolutionary origin of species can be a challenging task, especially when these species cross-breed and thereby cloud the genetic record of their evolution. Fast-developing techniques in acquiring genetic information have improved to the point where complete genomes can be routinely sequenced. One of the upcoming questions is how to make optimal use of this massive amount of data. This research project combines the above challenges, by using complete genomes of a group of cross-breeding cat species from Latin America. The objective is to optimize the use of vast genomic data to elucidate evolutionary history in a complex context of hybridization and other confounding processes. Various international partners are involved, and I will set up a close collaboration between the University of Antwerp and PUCRS, a Brazilian university with expertise in Neotropical carnivores. Part of the data required for this project is already available at PUCRS, where I contributed to the preliminary results that guide the two objectives of this project: (1) use complete genomes, including from museum specimens, to clarify the evolutionary relationships between the different species of small spotted cats in Latin America, and (2) complement the first objective with novel methods based on alternative genomic markers and partitions to maximize the amount of information that can be gained from these genomic sequences.

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Characterising genetic and phenotypic signatures of fisheries-induced life history evolution in commercially important Malawi cichlid fish. 01/11/2020 - 31/10/2022

Abstract

We currently lack a detailed understanding of how organisms rapidly adapt to environmental changes, which is key in evaluating and predicting human impact on nature, uncovering the genetic basis of adaptive traits, and gaining insight into fundamental evolutionary processes. Evolutionary response to a direct form of human impact, fishing,has often been discussed but evidence from natural systems is scarce. To address this, I will investigate genetic and phenotypic changes in Malawi cichlid fish following ~40 years of intense fishing. In particular, I will address life-history trait changes. Genome sequencing of museum specimens collected before and during fishing will give unprecedented insight into genes under selection. Extensive genomic resources available for Lake Malawi cichlids will allow me to investigate the evolutionary history of genes used in recent adaptation. I will leverage the ease of breeding cichlids in the lab to experimentally quantify genetic and environmental differences in traits implicated in fisheries-induced evolution. Furthermore, I will use state of the art (ancient) DNA and RNA sequencing technologies and bioinformatic methods to identify the genomic signature & molecular pathways involved in rapid life history adaptation. The combination of genome sequencing and controlled breeding experiments will greatly advance our understanding of how genomes can rapidly adapt to fishing and the link between selective pressures, phenotypes and genotypes.

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The molecular basis of human-induced life history adaptation. 01/10/2020 - 30/09/2024

Abstract

We currently lack a detailed understanding of how organisms rapidly adapt to environmental changes. However, gaining such an understanding is key in evaluating and predicting human impact on nature, can uncover the genetic basis of adaptive traits, and give insight into fundamental evolutionary processes. The most direct form of human impact on animal populations is hunting or fishing. Evolutionary responses to fishing have been often discussed, but direct evidence from natural systems is scarce. To address this, we will investigate genetic and phenotypic changes in Malawi cichlid fish following ~40 years of extremely intense fishing. We have recently produced genome sequencing data of 510 individuals of weakly and intensely fished populations from present day and from 18 years ago that will be analysed in this project. Combining this with innovative genome sequencing of museum specimens collected before and during fishing will give unprecedented insight into genes under selection. Furthermore, we will leverage the ease and relative speed of breeding cichlids in the lab to experimentally quantify genetic and environmental differences in traits life history traits implicated in fisheries-induced evolution. Integrating phenotypic measurement with the genomic differentiation measures into a quantitative genetics framework will allow us to directly test whether selection has acted on life history traits. Finally, we will characterise gene expression levels through transcriptome sequencing of tissues important in growth and maturation in weakly and intensely fished populations at different life stages. This will provide insight into adaptation at an important intermediate layer between genotypes and phenotypes. In summary, the combination of genome sequencing of recent and historic natural populations with controlled breeding experiments and transcriptome sequencing will greatly advance our understanding of the link between selective pressures, phenotypes and genotypes and has the potential to uncover how genomes can rapidly adapt to fishing.

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CALI-capture the light. 01/01/2020 - 31/12/2021

Abstract

The equipment applied for in this application is the Tecan SPARK®, a multimode microplate reader. The instrument reads microtiter plates up to 384 wells in various modes. Equipped with several monochromators, it measures optical density, several fluorescence modes and luminescence. It has an incubator-shaker ranging from 18° to 42°C. Unlike many other readers on the market, it is capable of measuring the quality and quantity of nucleic acids and proteins in volumes down to 2 microliters on 16 samples in parallel. It is a modular system which allows future extension with flash injectors, plate stacker, automatic lid removal etc… Prof. L. Bervoets (promotor), prof. G. De Boeck, and prof. H. Svardal (co-promotors) work in the SPHERE group on the effects of environmental stressors, both natural and anthropogenic, on the performance of aquatic and terrestrial organisms, in vivo and in vitro with an emphasis on mechanisms and ecological relevance. Prof. E. Prinsen (co-promotor) and the IMPRES group study plant stress and energy metabolism, acclimation mechanisms and the modelling of Leaf growth and tip growth and the role of plant hormones therein. All team members have an increasing need of in vitro assays to determine enzymatic activity and several other biomarkers such as hormones and cellular metabolites. The advanced possibilities of the SPARK® instrument offer several advantages, e.g. fluorescence modes, luminescence, scanning mode, etc., compared to the groups' current instruments (>10 years old). Notably, the cooling capacity of the incubator is unique on the market today. The facility for cooling is very important for the groups' research: SPHERE mainly focusses on the aquatic environment, and IMPRES on plants in a temperate climate, hence it is necessary to run assays at temperatures lower than typical room.

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Patterns of phenotypic similarity in the haplochromine cichlids of the Lake Victoria Region Superflock: an eco-morphological and genomic approach. 01/11/2019 - 31/10/2023

Abstract

Species that look very similar are not always closely related. Numerous examples of so-called convergent evolution have been reported: the flippers of penguins and dolphins, the wings of bats, birds, and insects, and the striking similarity between the eyes of humans and squids. Although structures look similar, the mechanisms of how they developed can be different. The Lake Victoria region (lakes Edward, Kivu, Albert, Victoria), is inhabited by 700 species of cichlids, a family of perch-like fishes that evolved very rapidly. Each of these species inhabits a single lake, and many species look very similar, both within a lake and between lakes. How they are related to each other has, however, remains unknown. Their young age and many similarities make these cichlids a perfect system to investigate how similar forms arise. Are they more closely related to each other or did they evolve independently from each other, and if so, which mechanisms underlie their similarity? For this, we will collect morphological and genomic data from 100 species from four distinct lakes. Similarities between species will be quantified, how similar species are related to each other will be genetically determined, and the regions of their DNA that contribute to their similarity will be determined. This will allow us to determine how these young species are related to each other and how similarities emerge within distinct species of cichlids from the Lake Victoria region.

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Charting the genomic landscape of hybridisation and genetic introgression across the Lake Malawi cichlid adaptive radiation. 01/11/2019 - 31/10/2023

Abstract

Recent genome studies suggest that hybridisation and genetic exchange among closely related species is more common than previously thought. Consequently, a central question in the study of biodiversity is the effect of genetic exchange on the formation and maintenance of species diversity. With more than 800 closely related species, the Lake Malawi cichlid fish adaptive radiation provides an intriguing model to study the frequency and evolutionary role of interspecific genetic exchange. Malinsky et al. (2018) found strong evidence for extensive gene flow early on in the Malawi radiation and made some links to adaptation. However, due to limitations in sampling and statistical inference methods, we are still lacking a comprehensive picture of the abundance and evolutionary role of genetic exchange in Malawi cichlids and in most other organisms. In this project I will establish a genomic framework for the joint inference of species relationships and genetic exchange, applying it to a unique dataset of more than 2000 genomes from 276 Malawi cichlid species to gain unprecedented insight into the abundance of genetic exchange between different populations, species and genera. Furthermore, I will refine a statistical method I developed during my Master's to test whether selection has acted on exchanged genetic material. In summary, this project will yield widely applicable genomic tools and insight into the role of gene flow in one of the most intriguing vertebrate radiations.

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Understanding the role of old genomic variation in rapid adaptation. 01/04/2019 - 31/03/2023

Abstract

The 100s of closely related but ecologically diverse species of Lake Malawi cichlid fishes provide an exceptional model to study the genomic mechanisms involved rapid adaptation and diversification. We have recently found that Lake Malawi cichlids harbour genomic regions of exceptionally high genetic diversity. In this project the student will analyse recently produced whole-genome sequencing data of 100s of Lake Malawi cichlid fish species to infer the evolutionary origin of genomic regions of high genetic diversity. For example, the student will test whether these genetic variants were brought into the ancestor of Lake Malawi cichlids by hybridisation with a divergent lineage of cichlid fish and whether this variation has been maintained by balancing selection. In a second step, the student will use population genetic methods to test for the role of these genetic variants in ecological adaptation and speciation of cichlid fish species. A specific application of this will be recent adaptation of populations to heavy fishing. Preliminary evidence suggests that genetic variation in regions of high ancestral diversity is under differential selection between weakly and heavily fished populations. The student will use statistical genomic techniques to test this systematically.

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Evolutionary, ecological and environmental omics. 01/10/2018 - 30/09/2023

Abstract

This funding will be used to initiate research projects as proposed in my tenure track ZAPBOF application and is intended to bridge the time between project start and acquisition of external research funding.

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Sequencing DNA of museum specimens to uncover the genetic basis of rapid adaptation to heavy fishing. 01/04/2019 - 30/03/2020

Abstract

We currently lack a detailed understanding of how organisms rapidly adapt genetically to environmental changes. However, gaining such an understanding is key in evaluating and predicting human impact on nature, can uncover the genetic basis of adaptive traits, and give insight into fundamental evolutionary processes. To address this, we will dissect the genetic factors contributing to rapid adaptation in Lake Malawi cichlid fish populations following ~40 years of extremely heavy fishing. We have already collected and whole-genome sequenced 96 samples from present day weakly and heavily fished populations. Analysis of these samples suggested overall very close relatedness between populations, but identified the presence of candidate genomic regions of high genetic divergence between weakly and heavily fished populations. Here we suggest to sequence the genomes of museum specimens (an innovative technique sometimes referred to as "museomics") from the same populations before the onset of heavy fishing and during fishing. Samples are available through established collaborations with the British Museum of Natural History, the Monkey Bay Fisheries Research Station in Malawi, and Prof. Erik Verheyen (University of Antwerp and Royal Belgian Institute of Natural Sciences). Comparing the genetic composition of historic populations with the present-day genetic composition (after 40 years of heavy fishing) will enable us to identify candidate genes conferring adaptation to fishing. We have performed a pilot study, which suggests that the museum specimens used in this study yield sufficient DNA for genome sequencing. We also have recently established breeding colonies of the same fish populations at the University of Antwerp, which will allow us in future projects to follow up phenotypic changes related to the genetic adaptations identified here. This project will yield important data and results to support an ERC starting grant application by the applicant on this study system that aims to dissect the links between genotypes, phenotypes and selective pressures in rapid human-induced evolution.

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