Evolutionary Immunogenomics

Molecular evolution of MHC and HLA, antigen presentation and peptidomics

My current research in the Evolutionary Immunogenomics group of Tobias Lenz at the University of Hamburg focuses on the evolution and diversity of the major histocompatibility complex, MHC, and its human counterpart, HLA.

I use computational and statistical approaches to study genomic diversity, molecular evolution and variation in antigen presentation. An important part of this work is the integration of genomic data with immunopeptidomic data, allowing us to investigate how genetic variation translates into differences in the peptides presented to the immune system.

My work also contributes to collaborative projects on host-pathogen interactions and immune-mediated disease. These projects connect evolutionary questions about immune diversity with biomedical questions involving infection, autoimmunity and immunotherapy.

More recently, my immunogenomic and evolutionary interests have again converged in the three-spined stickleback, where I investigate the molecular evolution and diversity of the MHC class II A and MHC class II B gene systems.

Another current research direction is the role of HLA variation during pregnancy. Within the Collaborative Research Centre CRC1713 "Maternal Immune Activation: Causes and Consequences", I contribute to project A06, which investigates how maternal and fetal HLA genotypes influence immune tolerance and susceptibility to infectious disease during pregnancy.

Across these projects, I combine immunogenomics, peptidomics, population genomics, phylogenomics, molecular evolution and computational biology.

Research group

Evolutionary Immunogenomics, University of Hamburg

CRC1713 - Maternal Immune Activation: Causes and Consequences

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Epigenetics of Ageing

From long-term wild populations to comparative avian epigenetic clocks

A major focus of my research is understanding how epigenetic variation changes with age in natural populations and how environmental and life-history differences influence biological ageing.

My work on common terns, together with Sandra Bouwhuis and collaborators at the Institute of Avian Research, uses repeated samples from individually known birds to investigate within-individual changes in DNA methylation across the lifespan. The long-term population at the Banter See in Wilhelmshaven allows molecular ageing patterns to be linked to detailed life-history information.

I extended this research to King penguins in collaboration with Emiliano Trucchi, Robin Cristofari and colleagues. Using epigenomic data from wild penguins, we investigated how differences in lifestyle and environmental exposure are associated with epigenetic ageing.

More recently, this work has expanded towards comparative approaches across birds, including the development of an avian epigenetic clock. Together, these projects aim to understand which molecular signatures of ageing are shared across species and which reflect the ecology and life history of particular populations.

Across my epigenetic projects, I also work on methodological questions in population epigenomics, including the benchmarking of sample-pooling strategies for natural populations.

Selected publications and projects

Lifestyle change accelerates epigenetic ageing in King penguins
The BEAC, an epigenetic clock for birds
Sex-specific changes in genome-wide methylation rate in ageing common terns
Benchmarking sample pooling for epigenomics of natural populations
Common Tern Project

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Stickleback Evolution

From local adaptation and epigenomics to the evolution of MHC class II

My work with three-spined sticklebacks began during my postdoctoral research at GEOMAR in the Marine Evolutionary Ecology group of Thorsten Reusch. I was part of the European BAMBI project, Baltic Sea Marine Biodiversity, an international and interdisciplinary project addressing the potential of marine organisms to adapt to environmental change in the Baltic Sea.

Using the three-spined stickleback as a model system, I investigated genetic and epigenetic variation among natural populations across environmental gradients. Together with Christophe Eizaguirre and collaborators, we studied how genomic variation and DNA methylation contribute to local adaptation, including responses to salinity and parasite exposure.

Multigenerational experiments with Melanie Heckwolf and collaborators extended this work to transgenerational plasticity and the adaptive potential of stickleback populations. More recently, I also contributed to research on the relationship between copy number variation and epigenetic diversity in natural stickleback populations.

I have now returned to stickleback research in the Evolutionary Immunogenomics group of Tobias Lenz at the University of Hamburg. My current work focuses on the molecular evolution and diversity of the stickleback MHC class II system, in particular MHC class II A and MHC class II B genes.

This long-term work on sticklebacks connects population genomics, epigenetics, local adaptation and immunogenomics within the same evolutionary model system.

Selected publications and projects

Two different epigenetic information channels in wild three-spined sticklebacks are involved in salinity adaptation
Experimental Parasite Infection Causes Genome-Wide Changes in DNA Methylation
Transgenerational plasticity and selection shape the adaptive potential of sticklebacks to salinity change
Copy number variation and epigenetic diversity
Evolutionary Immunogenomics, University of Hamburg

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Host-Pathogen Biology

Infection, immunity and immune-mediated disease

Alongside my evolutionary research, I contribute computational analyses to collaborative projects that investigate interactions between hosts, pathogens and the immune system.

These projects include research on tuberculosis, where host and pathogen factors can be analysed together to better understand variation in clinical disease, as well as work on the biology of the malaria parasite Plasmodium falciparum.

I have also contributed to research on immune-mediated disease and immunotherapy, including work on autoimmunity associated with checkpoint blockade. Together, these collaborations extend my interests in immunogenomics and molecular evolution into biomedical questions involving infection and immune regulation.

Selected publications

Host and pathogen factors modulate tuberculosis clinical severity independent of molecular bacterial burden
Disruption of a Plasmodium falciparum patatin-like phospholipase delays male gametocyte exflagellation
Autoimmunity against surfactant protein B is associated with pneumonitis during checkpoint blockade

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Migration Genomics

Population genomics and the evolution of migratory behaviour

Eurasian blackcaps are an exceptional system for studying the evolution of migration because populations show striking differences in migratory behaviour, ranging from long-distance migration to partial migration and residency.

In collaboration with Miriam Liedvogel and colleagues, I have contributed to genomic studies of blackcap populations with different migratory strategies. This work combines population genomic information with detailed knowledge of migration routes and individual behaviour obtained through long-term field studies and tracking.

A particular interest is the comparison of populations in which migratory behaviour has evolved differently, including island populations with independently evolved residency. Together with Andrea Bours and other collaborators, these natural contrasts provide an opportunity to investigate both population history and the genomic basis of behavioural variation.

The broader research programme combines genomics, behavioural ecology and migration tracking to understand how migratory phenotypes originate, persist and change during evolution.

Project and publication

Behavioural Genomics of Migration
Individual variability and versatility in an eco-evolutionary model of avian migration

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Cichlid Evolution

Phylogenetics, adaptive radiation, biogeography and immunogenetics of East African cichlid fishes

My doctoral research at the University of Basel in the group of Walter Salzburger focused on the evolutionary history of East African cichlid fishes, particularly the adaptive radiation of Lake Tanganyika.

I developed nuclear markers for multilocus phylogenetic analyses and used genomic multi-marker data to investigate relationships among the major cichlid lineages. Together with Walter Salzburger, Michael Matschiner and other collaborators, this work addressed the challenges that rapid diversification, incomplete lineage sorting and historical introgression pose for reconstructing species trees.

The same phylogenetic framework also contributed to studies of East African cichlid biogeography and to collaborative work on the evolution of cichlid egg-spots. In a further research direction, I investigated links between parasite communities, trophic ecology, morphology and MHC diversity across the Lake Tanganyika cichlid radiation.

Together, these projects combined phylogenetics, molecular evolution, evolutionary ecology and immunogenetics to study how one of the most diverse vertebrate radiations evolved.

Selected publications

A novel primer set for multilocus phylogenetic inference in East African cichlid fishes
A tribal level phylogeny of Lake Tanganyika cichlid fishes based on a genomic multi-marker approach
The evolution of cichlid fish egg-spots is linked with a cis-regulatory change
Back to Tanganyika: a case of recent trans-species-flock dispersal in East African haplochromine cichlid fishes
Disentangling Incomplete Lineage Sorting and Introgression to Refine Species-Tree Estimates for Lake Tanganyika Cichlid Fishes
An exploration of the links between parasites, trophic ecology, morphology, and immunogenetics in the Lake Tanganyika cichlid radiation

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