P. Hogeweg

Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities

The paper studies bacteriophage outbreaks in compost communities, finding that viral migration accelerates evolution through recombination and mutation spread.

Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis

This study uses a computational model to show how intracellular signaling evolved to resolve regulatory conflicts during mitochondrial endosymbiosis in eukaryogenesis.

Obligate Endosymbiosis Explains Genome Expansion During Eukaryogenesis

This paper constructs an evolutionary model of obligate endosymbiosis to study how it impacts genome evolution and cell-cycle coordination, finding that large host genomes and small symbiont genomes perform best over long timescales.

Evolution of Regulatory Complexity for Cell-Cycle Control

This study uses computational models to show that complex cell-cycle regulation evolves through adaptive network expansion and genomic organization, leading to distinct eco-evolutionary strategies.

Nothing in evolution makes sense except in the light of parasitism: evolution of complex replication strategies

This study shows that parasitism drives the evolution of complex replicators and ecosystems in RNA world models.

Slightly beneficial genes are retained by evolving Horizontal Gene Transfer despite selfish elements

The paper models how bacteria retain slightly beneficial genes through horizontal gene transfer despite the risks of selfish genetic elements, showing that spatial structure enables this retention.

Virtual Microbes evolve multiple mechanisms to the same end: anticipating a serial transfer protocol

The paper shows in silico evolved Virtual Microbes anticipate a serial transfer protocol through diverse mechanisms, showing both convergence and divergence in adaptation strategies.