Research Hannes Svardal

Abstract

Hybridisation between wild species and their domestic counterparts poses a large risk for the wild population. It may lead to the introduction of deleterious alleles that have been artificially selected for in the domestic species and even lead to complete genetic swamping of the wild genotype, resulting in a de facto extinction of the wild species. Conversely, hybridisation may also result in the introduction of adaptive alleles that provide a fitness advantage in the wild species context. Contact between the two species may also lead to an exchange of viruses, which could have severe health and epidemiological consequences in a non-natural host. The European wildcat (Felis silvestris) lives in close contact with, and is subject to hybridisation and potential virus exchange with its domestic congener (Felis catus). Understanding the patterns and drivers of introgression between these two species and the role of virus exchange will be vital for informing conservation efforts of the wildcat. To investigate this, I will collect whole-genome sequencing data from wildcats and apply statistical genomic algorithms to identify regions of adaptive introgression and purifying selection. Furthermore, I will characterise viral genomes from wildcats and use phylodynamics to test for virus exchange between the two species. To accomplish these goals, I will set up a collaboration between labs at the University of Antwerp and University of Liège that specialise in these types of analyses.

Researcher(s)

• Promoter: Svardal Hannes
• Co-promoter: Gryseels Sophie
• Fellow: Meeus Michaël

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

Although often genetically impoverished due to founder effects, inbreeding, genetic drift, and sequential bottlenecks, island populations tend to reach high densities and manage to adapt to the local environment. This is paradoxical because low allelic diversity can lead to inbreeding depression (reduction in fitness due to deleterious recessive alleles), and, on a longer timescale, to reduced genetic adaptability of populations. How and why do island populations, despite low genetic diversity, survive, adapt, and thrive? A first possibility might be that low heterozygosity does not translate into inbreeding depression through the purging of deleterious variants. Alternatively, the fitness consequences of inbreeding may be bearable under the mild selection regimes typical for islands. However, evidence that either of these mechanisms is at work in wild populations remains scarce. In this project, I will study the "island paradox" in insular and mainland populations of the Italian wall lizard, Podarcis siculus. For the first time, the relationships between population structure, genetic diversity, whole-animal performance, and selection gradients are integratively used to unravel how insular populations overcome genetic impoverishment.

Researcher(s)

• Promoter: Van Damme Raoul
• Co-promoter: Svardal Hannes
• Fellow: Van Linden Lisa

Research team(s)

• Functional Morphology

Project type(s)

• Research Project

Abstract

Adaptive radiations are showcases of evolutionary processes, characterised by rapid diversification of an ancestral lineage into an array of closely related species. We still don't understand how speciation, normally a slow process, can occur in such rapid 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.

Researcher(s)

• Promoter: Svardal Hannes
• Fellow: De Keyzer Els

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

High-throughput bio-analytical instruments generate an immense data flow. Translating these data into interpretable insights about the underlying processes of life and disease is increasingly dependent on bioinformatics techniques. Since 2012 BIOMINA (biomedical informatics network Antwerpen) brings together bioinformatics expertise, scattered over life science and computer science labs in our university, in an informal network. With this proposal we wish to transform this network, with its expertise and widely used infrastructure, into a BIOMINA core facility that can deliver a professional bioinformatics service. The mission is to 1) build a sustainable support, training, and collaboration model; 2) increase bioinformatics capacity to meet growing demands; and 3) build a strong bioinformatics community. It is proposed by complementary PIs in the field, to translate the available bioinformatics strengths to support biomedical, clinical, biological, and bioengineering labs within the University and external clients in hospitals and industry.

Researcher(s)

• Promoter: Laukens Kris
• Co-promoter: Mateiu Ligia Monica
• Co-promoter: Svardal Hannes
• Co-promoter: Van Camp Guy
• Co-promoter: Van Laere Steven

Research team(s)

• ADReM Data Lab (ADReM)

Project type(s)

• Research Project

Abstract

The expression of osteoderms (bony deposits embedded in the dermal layer of skin in vertebrates) is thought to provide many adaptive functions, including protection against predators or sexual rivals, and aiding in thermo- and hydro-regulation. Cordyline lizards are a subfamily of Southern African lizards that exhibit substantial variation in this adaptive trait. Within this group, the Cape cliff lizard (Hemicordylus capensis) shows extensive intrecific variation. However, little is known about the evolutionary basis for this variation. This project aims to unravel the genomic basis of variation in osteoderm expression in this species, using an integrative approach that combines genomic and transcriptomic methods with phenotypic data. To this end, genetic material will be collected in the field, allowing me to assemble a reference genome for this species and produce genomic data from populations that differ in their environments. I will combine these data with phenotypic data to test for associations between genomic differentiation and phenotypic variation. Furthermore, I will collect and analyse transcriptomic data to test for differential gene expression associated with osteoderm expression variation. Overall, this project will shed light on the evolutionary basis of an ecologically important functional trait. The high-quality genomic resources to be produced will provide useful tools for the research community.

Researcher(s)

• Promoter: Svardal Hannes
• Co-promoter: Laukens Kris
• Co-promoter: Van Damme Raoul
• Fellow: Leitão Henrique

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

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.

Researcher(s)

• Promoter: Svardal Hannes

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

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.

Researcher(s)

• Promoter: Van Damme Raoul
• Co-promoter: Laukens Kris
• Co-promoter: Matthysen Erik
• Co-promoter: Svardal Hannes

Research team(s)

• Functional Morphology

Project type(s)

• Research Project

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.

Researcher(s)

• Promoter: Svardal Hannes

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

Cryptobenthic clingfish of the genus Gouania are Mediterranean endemics. The genus currently includes five species that primarily separate along an axis of body elongation, with slender and stout morphotypes that independently evolved in the Adriatic Sea and the eastern Mediterranean basin. This makes Gouania an ideal model to study parallel evolution driven by strong natural selective forces on different levels such as genes, genomes, morphology or ecology. My PhD project builds upon promising and intriguing findings of my Bachelor's and Master's theses. As an important first step, I fixed the taxonomy of the genus Gouania, which also led to the first published chapter of my PhD thesis and forms the basis for further in depth investigation of this system. The second chapter of my PhD investigates the role of diverging microhabitat choices in sympatric Adriatic species of Gouania and the third illuminates the phylogenetic context of the Gouania radiation based on whole genomic data. Even though these previous chapters investigated crucial ecological and (macro)evolutionary factors that explain the diversity observed in Gouania, understanding and comparing the speciation potential of organisms unfolds best at a level of distinct populations within a species. This brings me to the host-group in Antwerp (Prof. Svardal) who is highly specialised in population genomic analyses. Therefore, for my final PhD chapter, which will be the major focus during my BOF funded stay in Antwerp, I aim to illuminate the drivers of local population structure of sympatric Gouania species, G. pigra and G. orientalis, from the island of Crete and an island closer to the mainland. Crete is interesting in this context, because it flanks two major marine biogeographic regions and is embedded in complex oceanographic circulation systems that show high seasonal fluctuations, which can drive population connectivity of marine animals. Gouania have a rather sedentary lifestyle as adults and dispersion can only happen during a short pelagic larval phase. Therefore, similar patterns of high geographic population structure would be expected in the investigated species. However, preliminary COI barcoding data suggests divergent population genetic patterns within the two species, whereby populations of G. orientalis from Crete seem to be more strongly isolated than G. pigra populations. By analysing whole genome population data from several sites, I aim to investigate microevolutionary processes in these two species such as population structuring, demographic history as well as recent events of hybridization and introgression (incl. their potential direction), to identify reasons for the contrasting patterns of geographic structure observed between the two species. My stay at the University of Antwerp will be crucial for this endeavour, because, having studied similar questions in other systems, Prof. Svardal and his group will provide essential expertise. Additionally, I will run Lagrangian simulations to model passive larval migration patterns, which will help to explain geographical structure observed in the dataset. Altogether, the results of this project will contribute to the general understanding of speciation and population dynamics of low-dispersing organisms in the marine realm, a group often neglected in the design and management of marine (protected) areas.

Researcher(s)

• Promoter: Svardal Hannes
• Fellow: Wagner Maximilian

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

The adaptive radiation of amphipods in Lake Baikal has brought forward more than 340 species (20% of the world's freshwater amphipods), making it one of the largest species flocks after the famous African cichlid radiations, and one of the only large radiations in temperate climates. Despite this iconic status the radiation has not yet been subject to detailed genomic investigation. During my PhD I was able to demonstrate excessive amounts of parallel adaptation among the transcriptomes of species of this adaptive radiation. In this project, I will use genomic approaches to test whether the previous results could be explained by hybridisation and adaptive introgression. These processes have been shown to occur in other adaptive radiations, but their functional role in rapid diversification is still debated. My preliminary resultsindicate that hybridization between two independent lineages of Baikalian amphipods emerged in the period when fast speciation started. Furthermore, I found intriguing signals of positive selection on introgressed loci. Additional data and specific methodology developed in this project will enable me to disentangle the processes governing speciation in this group. Profiting from strong relevant experience of the host laboratory I will re-analyze available transcriptomic datasets together with newly sequenced genomes. I will map precise directions of hybridization at the phylogenetic tree, describe functional associations of introgressed loci, test selection signatures associated with introgression, and estimate the extent to which repeatable ecomorphological traits are underpinned by "reusable" elements of ancestral genomes. This research has groundbreaking potential in providing a direct test of a potential catalysing role of hybridization in fast speciation in this system

Researcher(s)

• Promoter: Svardal Hannes
• Fellow: Burskaia Valentina

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

In this project, we empower local scientists to protect the unique biodiversity of the Malili Lake System, Sulawesi, through collaboration and training in innovative genomic methods to assess endemic biodiversity and its threats. We build partnerships to assess local biodiversity (species identification, delineation, distribution, abundance) and understand the ecological impact of invasive alien species. To ensure that our partner institute is on board with novel developments in genomics research and sequencing technology, we equip their lab for genome sequencing and provide in depth training through collaboration, internships, and workshops. We build a multi stakeholder partnership between involved research institutes, NGOs, local communities and local policy makers. The knowledge created in this project is made available to local communities through development and dissemination of educational materials. By increasing environmental literacy, we increase the personal and emotional involvement of local actors in nature and environment, empowering local actors to become agents of change.

Researcher(s)

• Promoter: Svardal Hannes

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

Abstract

Although often genetically impoverished due to founder effects, inbreeding, genetic drift and sequential bottlenecks, island populations tend to reach high densities and manage to adapt to the local environment. This is paradoxical because low allelic diversity can lead to inbreeding depression (reduction in fitness due to deleterious recessive alleles), and, on a longer timescale, to reduced genetic adaptability of populations. How and why do island populations, despite low genetic diversity, survive, adapt, and thrive? A first possibility might be that low heterozygosity does not translate into inbreeding depression, thanks to the mitigating effects of behavioural adaptations related to mate choice; or through the purging of deleterious variants. Alternatively, the fitness consequences of inbreeding may be bearable under the mild selection regimes typical for islands. However, evidence that either of these mechanisms is at work in wild populations remains scarce. In this project, I will study the "island paradox" in insular and mainland populations of the Italian wall lizard, Podarcis siculus. For the first time, the relationships between heterozygosity, physiological performance, behaviour, selection gradients and genomic structure are integratively used to unravel how insular populations overcome genetic impoverishment.

Researcher(s)

• Promoter: Van Damme Raoul
• Co-promoter: Svardal Hannes
• Fellow: Van Linden Lisa

Research team(s)

• Functional Morphology

Project type(s)

• Research Project

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.

Researcher(s)

• Promoter: Svardal Hannes
• Fellow: De Keyzer Els

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

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.

Researcher(s)

• Promoter: Svardal Hannes
• Fellow: Lescroart Jonas

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

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.

Researcher(s)

• Promoter: Svardal Hannes
• Co-promoter: De Boeck Gudrun
• Fellow: Hooft van Huysduynen Alexander

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

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.

Researcher(s)

• Promoter: Svardal Hannes
• Fellow: Sawasawa Wilson

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

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.

Researcher(s)

• Promoter: Bervoets Lieven
• Co-promoter: De Boeck Gudrun
• Co-promoter: Prinsen Els
• Co-promoter: Svardal Hannes

Research team(s)

Project website

Project type(s)

• Research Project

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.

Researcher(s)

• Promoter: Svardal Hannes
• Fellow: Gresham Sophie

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

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.

Researcher(s)

• Promoter: Svardal Hannes
• Co-promoter: Van Steenberge Maarten

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

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.

Researcher(s)

• Promoter: Svardal Hannes
• Fellow: Camacho Garcia Julia

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project

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.

Researcher(s)

• Promoter: Svardal Hannes

Research team(s)

Project type(s)

• Research Project

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.

Researcher(s)

• Promoter: Svardal Hannes
• Fellow: Svardal Hannes

Research team(s)

• Evolutionary ecology group (EVECO)

Project type(s)

• Research Project