Fabian Freund

Genomic variation and ancestry of Helicobacter pylori in the admixed population of Cabo Verde reveal host adaptation, limited host-pathogen ancestry concordance, and signatures of trans-Atlantic slave trade migrations

TMRCA is observable from the branch lengths of a coalescent

The paper develops a model-free estimator for the product of genealogical tree height and scaled mutation rate using site frequency spectra, showing it is unbiased and performs better than tree height averaging in simulations.

How many phage species remain undiscovered? Species sampling approaches to inform phage discovery

The paper estimates how many new phage species can be discovered based on existing databases and identifies changes in species abundance over time.

Muller's Ratchet and Gene Duplication

The paper models duplication-selection dynamics in gene families, showing that finite populations experience unbounded copy number growth unless counteracted by synergistic epistasis.

Population genomics and molecular epidemiology of wheat powdery mildew in Europe

This study analyzes the population genomics and molecular epidemiology of wheat powdery mildew in Europe, revealing population structure linked to wind patterns and identifying loci under selection, including fungicide targets and avirulence genes.

Simultaneous Inference of Past Demography and Selection from the Ancestral Recombination Graph under the Beta Coalescent

This paper introduces two methods to infer demographic history and selection from sequence data by modeling the ancestral recombination graph under the beta coalescent.