Previous work [10, 11] has studied models of within-host evolution and between-host transmission, in which an initially poorly transmitting pathogen acquires adaptations to human hosts, following repeated zoonotic introductions until it achieves pandemic potential. These make the natural, simplifying assumption that the host population is homogeneous, so that changes in infection parameters entirely reflect adaptations in the biology of host infection. In reality, however, factors such as human contact patterns [12] and other host heterogeneity [13, 14] may also shape the risk and speed of emergence events. We concentrate here on the heterogeneity in the spatial structure of the human host population, an area which has hitherto received little attention in the context of adapting pathogens. We model spatially separated communities with varying types and strengths of interconnections, for example between a village and a city. Our aim is to study under what regimes such 'ecological' structure could have a strong effect on emergence, in comparison with 'evolutionary' factors governing the biology of infection.