We are exited to offer a fully funded PhD position focused on 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 accross 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 occured through parallel evolution or a shared genetic innovation.  Promising regulatory elements will be functionally validaded 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. 

We are looking for a highly motivated PhD candidate with :

• A strong academic track record
• Enthusiasm for evolutionary ecoloy, 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. For more information please contact Prof. dr. Steven Van Belleghem, tel.: +32 16 32 79 71, mail: steven.vanbelleghem@kuleuven.be or Mrs. Conny Coeckelberghs, tel.: +32 16 32 37 17, mail: conny.coeckelberghs@kuleuven.be or Markus Moest, mail : markus.moest@uibk.ac.at