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Mutualism evolution and stability are major outstanding questions in evolutionary biology. To address these questions, I have adopted subterranean ant-trophobiont-microbe interaction networks as a study system. My research is organised into three empirical and one theoretical research lines, and employs a broad range of methods, from computer simulation to advanced microscopy, field sampling, high-throughput sequencing and behavioural experiments. With all these combined, I aim to contribute to a better understanding of the emergence and persistence of cooperation between species.