Research Els De Keyzer

Abstract

Understanding speciation is a central question in evolutionary biology and is crucial for conservation amidst global biodiversity changes. Adaptive radiations have been a significant driver of Earth's biodiversity. The adaptive radiation of sailfin silversides (Telmatherina) in the Malili Lakes of Sulawesi, Indonesia—termed "Wallace's Dream Ponds"—provides an excellent model for studying speciation processes, especially as ongoing hybridization events in these silversides allow investigation into the role of genetic exchange in speciation. The Malili Lakes system is under imminent threat from human activities, including invasive species, notably the invasive flowerhorn cichlid, highlighting the urgency of the proposed research. Through whole-genome sequencing, my postdoctoral research revealed complex relationships among the silverside species in Lake Matano, including significant mito-nuclear discordance and evidence of ongoing introgression from the riverine species Telmatherina bonti. Interestingly, introgression from T. bonti appears strongest near the lake-river interface, creating a spatial gradient of introgression within Lake Matano. This proposal aims to capitalize on this interesting finding by examining speciation dynamics in closely related Lake Matano silversides, T. opudi and T. sarasinorum. These species are phenotypically distinct yet genetically similar, with incomplete reproductive isolation. I hypothesize that introgression with T. bonti could either homogenize these species (if similar alleles are retained) or promote further divergence (if different alleles are favored in distinct ecological niches). To test this, I will compare introgression patterns across spatially distinct populations within Lake Matano, assessing whether similar or different introgressed regions are retained in T. opudi and T. sarasinorum as the distance from the hybrid zone increases. Methodology The study will sample 20 individuals of T. bonti from an upstream, non-introgressed river population and 120 individuals of T. opudi and T. sarasinorum from both the hybrid zone and four locations increasingly distant from it. Whole-genome sequencing (150 bp paired-end, at 8x coverage) will be conducted, balancing cost with depth. Leveraging the power of in-house developed tools such as Dinvestigate (part of Dsuite), I will identify introgressed genomic regions and compare them across the spatial gradient. More overlap in retained regions would suggest a homogenizing effect of introgression, while less overlap would indicate divergent selection acting on introgressed alleles, which would be a strong indication that introgression could facilitate divergence between T. opudi and T. sarasinorum. Relevance This study will directly test the impact of hybridization with a third species on speciation, a novel approach within a natural vertebrate system. Given the conservation concerns surrounding the Malili Lakes, this research will provide insights valuable for comparing pre- and post-invasion speciation dynamics. Furthermore, collaborating with Indonesian researchers enhances both local and international scientific capacity for conservation genomics. Future Impact Building on my postdoctoral research, this project contributes to establishing Lake Matano's silverside radiation as a model system for studying the role of hybridization in biodiversity formation. This research will support my development as an independent researcher and lay a foundation for future investigations into the effects of introgression on speciation. The expected results, whether introgression facilitates or hinders speciation, will open new avenues for research, high-impact publication, and collaborative networks, particularly in Indonesia. This funding will enable a focused investigation into a novel pattern of spatial introgression, advancing our understanding of speciation mechanisms in the context of threatened adaptive radiations.

Researcher(s)

• Promoter: De Keyzer Els

Research team(s)

• Evolutionary ecology group (EVECO)

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

The emergence of biodiversity through evolution is a defining question in evolutionary biology and instrumental in conservation in the face of global biodiversity change. Much of the evolution of biodiversity on Earth was driven by adaptive radiations – bursts rapid speciation over relatively short evolutionary timescales. Ongoing adaptive radiations allow us to study the rapid emergence of biodiversity in real time. The Malili Lakes in central Sulawesi, Indonesia, also called Wallace's Dream Ponds, are a diversity hotspot, supporting multiple adaptive radiations and high degrees of endemism in various groups, such as snails, shrimp, crabs, and fish. One of these adaptive radiations, the sailfin silverside fishes (genus Telmatherina) have diversified in the lakes producing ~20 species and morphotypes with many different phenotypic and ecological adaptations. While these sailfin silverside fishes have been well characterised ecologically and morphologically, their genomes have not yet been investigated and their evolutionary relationships are still largely unresolved. During the past year, analysing whole genome sequencing data, I found that three of the species of sailfin silverside fishes form a hybrid swarm, meaning they continually hybridise, while remaining distinct species. My own analysis during the first year of my post-doctoral research has shown that these three species are more difficult to distinguish on a genomic level than previously anticipated. Therefore, I now request funding to sequence 60 additional samples (20 of each of these three species), to identify genomic regions of differentiation between the three species. In this project, I will perform a detailed genomic characterisation of the differences and similarities between the pure (not hybridised) forms of these three species. Using whole genome sequences of 20 individuals of each of the three species, I will construct the genomic landscapes of divergence between species pairs of pure (non-hybridised) individuals, by calculating divergence statistics such as dxy and FST, over small windows of the genome. This will allow me to identify regions which show genomic peaks of species divergence (high values of FST or dxy), and 'valleys' of low divergence (high similarity). This funding specifically will allow me to uncover information about the genomes of three of the species which are the focus of my post-doctoral research. The results on the genomic architecture of and the landscapes of divergence between these three fish species will be indispensable for the correct interpretation of my results throughout all the publications of my post doc and beyond. Being the first genomic investigation of an enigmatic and threatened adaptive radiation in an understudied diversity hotspot and taking steps towards addressing a cutting-edge research question, the results of this project will be of major scientific interest. This project will help me with setting up this study system, and gaining skills for genomic analysis, which are important steps towards developing my own line of research building on my post-doctoral research.

Researcher(s)

• Promoter: De Keyzer Els

Research team(s)

• Evolutionary ecology group (EVECO)

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