Alex Zemella

Forschungsgruppe Küpper
MPI für Ornithologie Seewiesen


I have a keen interest in the application of the most cutting-edge -omics technologies to non-model organisms to improve our understanding of these species and answer fundamental evolutionary and ecological questions. Notably, I recently became interested in RNA-Sequencing and data analysis methods to measure gene expression in different tissues or conditions.

The Ruff (Calidris pugnax) represents a unique model system of adaptive phenotype diversification, with three different morphs (Independent, Satellite and Faeder) that differ in size, physiology, behaviour and plumage. These three different breeding phenotypes are fully genetically determined by a 4.4 Mbp long autosomal inversion region located on chromosome 11 that arose hundreds of thousands of years ago. Chromosomal inversions provide compelling examples of how the re-organization of genomic structure may lead to an increase in phenotypic diversity within and between species.

In my current project, I investigate how the autosomal Ruff inversion affects gene expression and regulation across both the three male mating morphs and different life stages. In particular, I am targeting tissues that are important for steroid synthesis or associated with aggression and courtship behaviour (e.g. brain and gonads) to examine how the aforementioned autosomal inversion leads to variation in male aggression and courtship. To this end, I will compare the expression of autosomal genes located inside and outside the inversion across the three mating morphs. I will also identify co-expression networks of genes with similar expressions to determine the modular structure of transcriptional responses. I also plan to investigate whether and how alternative splicing and chromatin availability are affected by the autosomal inversion. Finally, I will compare variation in gene networks associated with aggression and courtship between morphs across three critical stages of ontogeny.


·       2021 - Present: PhD, Max Planck Institute for Ornithology (Research Group Küpper), Seewiesen, Germany

·     2018 - 2021: MSc, Marine Biology, University of Bologna, Italy. Thesis Title: “Functional annotation of the brown skate (Raja miraletus Linnaeus, 1758) transcriptome and differential gene expression analysis of pigmentary genes in five skate species”

·    2014 - 2018: BA, Natural Sciences, University of Bologna, Italy. Thesis Title: “Meiobenthic assemblages associated with mussel beds on different substrates in the Ravenna harbour"

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