Rice yellow mottle virus in Madagascar and in the Zanzibar Archipelago; island systems and evolutionary time scale to study virus emergence

► Island systems and evolutionary time scales are used for the first time in combination to study virus emergence. ► Robust estimates of the dates of introductions of RYMV in Madagascar and Zanzibar are obtained from heterochronous sequences. ► Spread of RYMV across Africa results from frequent dissemination over tens of kilometers and rare dispersal events over hundreds of kilometers.