Nucleotide sequences of P3 and pipo genes of Potato virus Y (PVY) from potato and tobacco were compared to investigate the effect of hosts on the population genetic structure. Meanwhile, mutation, natural selection and gene flow were evaluated to determine evolutionary forces responsible for the population genetic dy-namics. The fixation indices of population differentiation (F ST ) of PVY from tobacco and potato were 0.116 and 0.120, respectively with significant difference, suggesting a moderate genetic differentiation between the two popula-tions. Genetic variation analysis showed that nucleotide identities in P3 and pipo genes among the viral isolates from tobacco were respectively in the range of 85.2%−100%and 76.5%−100%while that from potato were respectively in the range of 95.7%−100%and 93.0%−100%, indicating higher genetic variation in PVY from tobacco than that from potato. Moreover, purifying selection was detected on the majority of polymorphic sites within P3 gene, suggesting that most of mutations in the gene were harmful and consequently being eliminated by natural selection. Conversely, positive selection was detected on two polymorphic sites, suggesting that these two mutations were beneficial to PVY. Neither purifying nor positive selection was detected in pipo gene, indicating neutral evolution of the gene. The values of gene flow (Nm) between PVY populations from tobacco and potato in P3 and pipo genes were 1.91 and 1.83, respec-tively, suggesting strong gene flow also contributes significantly to the population genetic dynamics of PVY popula-tion. In summary, this study indicates there was a significant genetic variation in PVY hosted by tobacco and potato, and mutation, natural selection and gene flow all contribute to the genetic diversity and population dynamic of the virus.%文章以马铃薯Y病毒(Potato virus Y, PVY) P3和pipo基因为分子标记，比较分析烟草和马铃薯两个寄主的PVY遗传多样性和群体分化，并评估突变、选择、基因流等遗传力所起的作用。通过P3和pipo基因计算获得的烟草和马铃薯群体分化指数FST分别为0.116和0.120，且统计检验差异显著，表明烟草和马铃薯寄主的PVY之间中度分化。变异分析结果显示，烟草分离物P3和pipo基因的核苷酸序列一致性分别为85.2%~100%和76.5%~100%，而马铃薯分离物的P3和pipo基因的核苷酸序列一致性分别为95.7%~100%和93.0%~100%，表明烟草PVY变异程度高于马铃薯。同时，P3基因内检测到大量的净化选择位点，表明该基因大部分位点的变异为有害突变，在进化过程中被剔除。此外，P3基因内还检测到两个显著正向选择位点，表明这两个位点的变异为有益突变，有利于病毒的生存竞争。在pipo基因中未检测到显著的选择位点，表明该基因上的变异基本不受自然选择影响。通过P3和pipo基因计算烟草和马铃薯群体间的基因流Nm值分别为1.91和1.83，表明这两个群体间存在较强的基因交流。以上结果表明，来源于烟草和马铃薯寄主的PVY遗传差异显著，突变、自然选择以及基因流都影响两者的遗传多样性及遗传分化程度。
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