The biogeography of viral emergence: rice yellow mottle virus as a case study

•The key role of the early steps of rice intensification in the emergence of RYMV in Africa.•In East Africa, virus emergence followed rice intensification and extension.•In West Africa, the contrasted history of rice differently shaped virus populations.

Rice yellow mottle virus (RYMV) exemplifies the key role in plant virus emergence of the early steps of crop extension and intensification in traditional agriculture. In East Africa, RYMV emerged in the 19th century after rice intensification along the Indian Ocean coast, and later spread inland concomitantly with rice introduction. In West Africa, the contrasted history of rice cultivation among regions differently shaped RYMV populations. A biogeographical approach — which jointly considers the spatial distribution of the virus and its hosts over time — was applied to reach these conclusions. We linked the evolution of RYMV over the past two centuries to a geographical map of the history of rice cultivation in Africa.