The diversification of begomovirus populations is predominantly driven by mutational dynamics

Begomoviruses (single-stranded DNA plant viruses) are responsible for serious agricultural threats. Begomovirus populations exhibit a high degree of within-host genetic variation and evolve as quickly as RNA viruses. Although the recombination-prone nature of begomoviruses has been extensively demonstrated, the relative contribution of recombination andmutation to the genetic variation of begomovirus populations has not been assessed.We estimated the genetic variability of begomovirus datasets from around the world. An uneven distribution of genetic variation across the length of the cp and rep genes due to recombination was evident from our analyses. To estimate the relative contributions of recombination andmutation to the genetic variability of begomoviruses, we mapped all substitutions overmaximum likelihood trees and counted the number of substitutions on branches which were associated with recombination (gr) andmutation (gl). In addition, we also estimated the per generation relative rates of both evolutionarymechanisms (r/l) to express how frequently begomovirus genomes are affected by recombination relative tomutation. We observed that the composition of genetic variation in all begomovirus datasets was dominated by mutation. Additionally, the low correlation between the estimates indicated that the relative contributions of recombination andmutation are not necessarily a function of their relative rates. Our results show that, although a considerable fraction of the genetic variation levels could be assigned to recombination, it was always lower than that due tomutation, indicating that the diversification of begomovirus populations is predominantly driven bymutational dynamics.