Within plant populations, individual plants host viruses. Viruses have associations with each other, either through direct mutualistic or antagonistic interactions (bold font); indirect associations mediated by another virus, shared vector, and/or host immunological responses (small font); or other effects operating at the host plant level. The environment can influence the (co-)occurrences either directly or through host effects at the level of host populations or individuals, or via vectors (capital font). The solid arrows represent direct associations between two viruses, whereas the dashed arrows show the indirect associations. The additional conditioning explanatory variables included in our constrained models are illustrated (capital font). The indirect effects (mediator species and changes and variation in host immune response, small font) are included in the models implicitly through spatial variables and the model structure. SeeTable 1for details on the additional conditioning variables.
