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; NP), central Japan, where several hundred sika deer (Cervus nippon) have been protected for more than 1,200 years, heavily- or moderately-haired nettle (Uritica thunbergiana) populations have evolved probably in response to intense deer browsing. Here, we analysed the genetic structure of two populations from NP and five from surrounding areas 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, Bayesian clustering and principal coordinates analyses using all-loci, non-outlier loci and outlier loci datasets showed that the two populations from NP formed a cluster distinct from the surroundings. These results indicate the genome-wide differentiation of the populations from NP and the surroundings. Moreover, these imply that: (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 NP. This study suggests that a single herbivore species could lead genetic differentiation among plant populations.

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 km 2 ), 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.