PhD Position in Evolutionary and Molecular Ecology Link to apply: https://www.kuleuven.be/personeel/jobsite/jobs/60500112 Project Overview We are excited to offer a fully funded PhD position focused on the ecology, evolution, and molecular mechanisms of plasticity and adaptation in Daphnia, with a particular emphasis on melanistic Daphnia zschokkei from alpine lakes. The project combines fieldwork, genomics, transcriptomics, and functional experiments to answer fundamental questions in evolutionary biology. Suggested research questions (RQs): * RQ1: Evolution and taxonomic status of Daphnia zschokkei Several Daphnia species and ecotypes display melanization, yet the evolutionary history of this adaptive phenotype remains largely unresolved. Daphnia zschokkei, a melanized taxon inhabiting alpine lakes, was originally described as a distinct species but is currently treated as an ecotype of D. longispina, based on single-locus and microsatellite data. However, preliminary whole-genome analyses suggest that these melanized populations may form a distinct genetic cluster. This project aims to determine whether melanization evolved once and spread across the Alps, or arose repeatedly from local D. longispina populations. Whole-genome sequencing of melanized "zschokkei" and non-melanized D. longispina across a wide geographic range will be used to resolve phylogenetic relationships, clarify taxonomic status, and reconstruct the evolutionary origins of this trait. Including other melanized populations from the D. longispina complex will allow broader inferences about the evolution of melanization. * RQ2: Quantifying variation in melanization Melanization can be constitutively expressed or environmentally induced. To better understand variation in this trait, we will collect clonal lineages from multiple D. zschokkei populations (as part of RQ1), measure melanization levels in the field, and rear the clones under standardized lab conditions for several generations. This will allow us to determine baseline levels of constitutive expression. After baseline quantification, clones will be exposed to UV treatments to assess plastic responses. Environmental data from each site (UV exposure, turbidity, depth, nutrient levels, predator abundance) will be integrated to assess which factors best explain phenotypic variation. * RQ3: Genetic basis and regulatory architecture of melanin expression Initial findings suggest that melanization in D. zschokkei is largely plastic, implicating regulatory mechanisms. By integrating whole-genome data (RQ1) and phenotypic data (RQ2), we will perform genome-wide association studies, outlier detection, and selection scans to identify candidate genes and regulatory elements involved in melanization. In selected populations, we will conduct controlled induction experiments and collect samples for RNA-seq and ATAC-seq to identify expression patterns and accessible chromatin regions linked to regulatory variation. This integrative approach will help distinguish between constitutive and inducible components of melanization and test whether adaptation occurred through parallel evolution or a shared genetic innovation. Promising regulatory elements will be functionally validated using CRISPR/Cas9 in collaboration with partner labs. * RQ4: Comparative genomics of melanin regulation in Daphnia Melanized forms are also found in several species within the D. pulex complex, such as D. melanica, D. tenebrosa, and D. middendorfiana. Using the approaches developed in RQ3, we will identify candidate genes and regulatory elements in these taxa and compare them to findings from the D. longispina complex. This comparative framework will illuminate whether similar genetic mechanisms underlie melanization across Daphnia lineages. Candidate Profile We are looking for a highly motivated PhD candidate with: * A strong academic track record * Enthusiasm for evolutionary ecology, population genetics and functional genomics * Bioinformatics skills * Excellent command of written and spoken English This is a full-time position initially offered for one year, with the possibility of extension up to four years. Research Environment You will be jointly supervised by Prof. Steven Van Belleghem at KU Leuven (Belgium) and Prof. Markus Moest at the Research Institute for Limnology, University of Innsbruck (Austria), located on the shores of Lake Mondsee. * The research group of Steven Van Belleghem (KU Leuven) focuses on eco-evolutionary and functional genomics in a variety of systems. Website: https://bio.kuleuven.be/eeb/sv * The research group of Markus Moest (Mondsee) specializes in the ecology and evolution of the D. longispina group. The institute provides state-of-the-art infrastructure for Daphnia fieldwork, culturing, and experimental biology. Markus Moest's extensive network across the Alps will facilitate a wide-reaching and efficient sampling campaign. Website: https://www.uibk.ac.at/limno/personnel/moest/index.html.en Life in Leuven and Mondsee Leuven is a vibrant, historic university city offering a high standard of living, excellent public transport, and a strong international community. It's only 15 minutes from Brussels Airport and under two hours by train from Paris, Amsterdam, and London. KU Leuven, founded in 1425, ranks consistently among Europe's top research universities. Mondsee is a picturesque lakeside town in the Salzkammergut region of Austria, surrounded by the Alps. The Research Institute for Limnology provides a stunning research setting with a strong focus on freshwater ecology and evolutionary biology. Application Process Please send your application as a single PDF file including: * A CV * A 1-page motivation letter (including relevant research experience) * Transcripts of your bachelor's and master's degrees * Contact details of two academic references Submit your application via the KU Leuven online platform and send it by email to both: * Steven Van Belleghem: Steven.VanBelleghem@kuleuven.be * Markus Moest: Markus.Moest@uibk.ac.at Subject line: PhD_Application_YOURNAME Deadline: 31 July 2025 Start date: 1 October 2025 (negotiable) Commitment to Diversity KU Leuven is committed to creating an inclusive environment where all talents can thrive, regardless of gender, age, cultural background, nationality, or disability. For questions about accessibility or support, contact: diversiteit.HR@kuleuven.be Steven Van Belleghem (to subscribe/unsubscribe the EvolDir send mail to golding@mcmaster.ca)