Many studies have inferred the way in which natural selection, genetic drift and gene flow shape the population genetic structures, but very few have quantified the population differentiation under spatially and temporally varying levels of selection pressure, population fluctuation and gene flow. In Nara Park (6.6 km²), central Japan, where several hundred sika deer (Cervus nippon) have been protected for more than 1,200 years, heavily- or moderately-haired nettle (Urtica thunbergiana) populations have evolved probably in response to intense deer browsing. Here, we analysed the genetic structure of two Nara Park populations and five surrounding populations using amplified fragment length polymorphism markers. A total of 546 marker loci were genotyped from 210 individuals. A Bayesian method estimated 5.5% of these loci to be outliers, which are putatively under natural selection. Neighbour-joining, principal coordinates and Bayesian clustering analyses using all-loci, non-outlier loci and outlier loci datasets showed that the Nara Park populations formed a cluster distinct from the surroundings. These results indicate the genome-wide differentiation of the Nara Park populations from the surroundings. Moreover, these imply the following: (1) gene flow is limited between these populations and thus genetic drift is a major factor causing the differentiation; and (2) natural selection imposed by intense deer browsing has contributed to some extent to the differentiation. In conclusion, sika deer seems to have counteracted genetic drift to drive the genetic differentiation of hairy nettles in Nara Park. This study suggests that a single herbivore species could lead to genetic differentiation among plant populations.

许多研究已经推断出自然选择、遗传漂变和基因流动塑造种群遗传结构的方式，但很少有研究在选择压力、种群波动和基因流动的时空变化水平下量化种群分化。在日本中部的奈良公园（6.6 公里²），数百只梅花鹿 ( Cervus nippon ) 已被保护了 1200 多年，重度或中度毛荨麻 ( Urtica thunbergiana )) 种群的进化可能是为了应对强烈的鹿浏览。在这里，我们使用扩增的片段长度多态性标记分析了两个奈良公园种群和五个周围种群的遗传结构。对来自 210 个个体的总共 546 个标记基因座进行了基因分型。贝叶斯方法估计这些基因座中有 5.5% 是异常值，它们被推定在自然选择之下。使用所有基因座、非离群基因座和离群基因座数据集的邻接、主坐标和贝叶斯聚类分析表明，奈良公园人口形成了一个不同于周围环境的集群。这些结果表明奈良公园种群与周围环境的全基因组分化。此外，这些意味着以下内容：(1) 这些种群之间的基因流动受到限制，因此遗传漂变是导致分化的主要因素；(2) 强烈的鹿食引起的自然选择在一定程度上促成了分化。总之，梅花鹿似乎抵消了遗传漂变，从而推动了奈良公园毛荨麻的遗传分化。这项研究表明，单一的食草动物物种可能导致植物种群之间的遗传分化。