Abstract 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 and mutation 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 and mutation to the genetic variability of begomoviruses, we mapped all substitutions over maximum likelihood trees and counted the number of substitutions on branches which were associated with recombination (ηr) and mutation (ημ). In addition, we also estimated the per generation relative rates of both evolutionary mechanisms (r/μ) to express how frequently begomovirus genomes are affected by recombination relative to mutation. 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 and mutation 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 to mutation, indicating that the diversification of begomovirus populations is predominantly driven by mutational dynamics.

中文翻译：

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Begomovirus 种群的多样化主要由突变动力学驱动

摘要 Begomoviruses（单链 DNA 植物病毒）是造成严重农业威胁的原因。Begomovirus 种群表现出高度的宿主内遗传变异，并且与 RNA 病毒一样快速进化。尽管贝戈莫病毒的重组倾向性已被广泛证明，但尚未评估重组和突变对贝戈莫病毒种群遗传变异的相对贡献。我们估计了来自世界各地的 begomovirus 数据集的遗传变异性。从我们的分析中可以明显看出，由于重组，cp 和 rep 基因长度上的遗传变异分布不均匀。为了估计重组和突变对 begomoviruses 遗传变异性的相对贡献，我们将所有替换映射到最大似然树上，并计算与重组 (ηr) 和突变 (ημ) 相关的分支上的替换数量。此外，我们还估计了每代进化机制 (r/μ) 的相对速率，以表达 begomovirus 基因组受重组相对于突变影响的频率。我们观察到所有 begomovirus 数据集中的遗传变异组成以突变为主。此外，估计值之间的低相关性表明重组和突变的相对贡献不一定是它们相对速率的函数。我们的结果表明，虽然相当一部分的遗传变异水平可以分配给重组，但它总是低于由于突变引起的水平，