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An important challenge in theoretical ecology is to better predict ecological responses to environmental change, and in particular to spatial changes such as habitat fragmentation. Classical food-web models have focused on purely ecological predictions, without taking adaptation or evolution of species traits into account. We address this issue using an eco-evolutionary model, which is based on body masses and diets as the key traits that determine metabolic rates and trophic interactions. The model implements evolution by the introduction of new morphs that are related to the existing ones, so that the network structure itself evolves in a self-organized manner. We consider the coupling and decoupling of habitats in multi-trophic metacommunities consisting of 2 or 4 habitats. Our model thus integrates metacommunity models, which describe ecosystems as networks of networks, with large community evolution models. We find that rescue effects and source-sink effects occur within coupled habitats, which have the potential to change local selection pressures so that the local food web structure shows a fingerprint of its spatial conditions. Within our model system, we observe that habitat coupling increases the lifetimes of top predators and promotes local biodiversity.