The long-term coevolution of hosts and pathogens in their environment forms a complex web of multi-scale interactions. Understanding how environmental heterogeneity affects the structure of host–pathogen networks is a prerequisite for predicting disease dynamics and emergence. Although nestedness is common in ecological networks, and theory suggests that nested ecosystems are less prone to dynamic instability, why nestedness varies in time and space is not fully understood. Many studies have been limited by a focus on single habitats and the absence of a link between spatial variation and structural heterogeneity such as nestedness and modularity. Here we propose a neutral model for the evolution of host–pathogen networks in multiple habitats. In contrast to previous studies, our study proposes that local modularity can coexist with global nestedness, and shows that real ecosystems are found in a continuum between nested-modular and nested networks driven by intraspecific competition. Nestedness depends on neutral mechanisms of community assembly, whereas modularity is contingent on local adaptation and competition. The structural pattern may change spatially and temporally but remains stable over evolutionary timescales. We validate our theoretical predictions with a longitudinal study of plant–virus interactions in a heterogeneous agricultural landscape.

宿主和病原体在其环境中的长期协同进化形成了复杂的多尺度相互作用网络。了解环境异质性如何影响宿主-病原体网络的结构是预测疾病动态和出现的先决条件。尽管嵌套在生态网络中很常见，并且理论表明嵌套的生态系统不太容易发生动态不稳定，但为什么嵌套在时间和空间上变化的原因尚不完全清楚。许多研究受到局限在单一栖息地上以及空间变化与结构异质性（如嵌套性和模块性）之间缺乏联系的限制。在这里，我们为多种生境中宿主-病原体网络的进化提出了一个中性模型。与以前的研究相比，我们的研究提出，局部模块化可以与全局嵌套共存，并表明在种内竞争驱动的嵌套模块和嵌套网络之间的连续体中可以找到真实的生态系统。嵌套取决于社区集会的中立机制，而模块化则取决于本地的适应和竞争。结构模式可能会在空间和时间上发生变化，但在进化时标上保持稳定。我们通过对异种农业景观中植物与病毒相互作用的纵向研究来验证我们的理论预测。而模块化则取决于当地的适应和竞争。结构模式可能会在空间和时间上发生变化，但在进化时标上保持稳定。我们通过对异种农业景观中植物与病毒相互作用的纵向研究来验证我们的理论预测。而模块化则取决于当地的适应和竞争。结构模式可能会在空间和时间上发生变化，但在进化时标上保持稳定。我们通过对异种农业景观中植物与病毒相互作用的纵向研究来验证我们的理论预测。