New insights in the evolutionary history of cacao-infecting badnaviruses

The cacao crop spread throughout the world from its center of origin in South America. However, one of its main diseases cacao swollen shoot disease (CSSD), which is caused by the complex of cacao-infecting badnaviruses, was first detected in Africa. Here we investigate the relationship between the genetic diversity of the viruses that cause CSSD and their geographical distribution, and the possible relationship between the genetic diversity of the virus and the symptoms they trigger. We also sought to determine the evolutionary models that could explain this relationship and evaluate the evolutionary history of the virus through ancestral state reconstructions and temporality analyses. A high mutation rate was observed along with a clear phylogenetic signal in the geographic distribution and in the symptoms associated with each viral species. The molecular clock provided new evidence on the emergence and speciation of cacao-infecting badnaviruses, suggesting a possible American origin of these viruses. •A high mutation rate was observed of the CSSV species.•Geographical region and Symptoms traits showed a clear phylogenetic signal.•In Africa, Ghana was found as the center of virus dispersal.•CSSV possibly originated from America.•The evolutionary history of CSSD together with cacao spread was reconstructed.