The increasing deer population and their expanding distribution have altered the diversity and biomass of the plant community in the northern hemisphere. Furthermore, anthropogenic disturbances such as nitrogen deposition and logging threaten plant diversity in many parts of the forests. Therefore, it is necessary to investigate the effects of deer on plant communities under nitrogen deposition and logging conditions to understand and conserve plant diversity in forest ecosystems. We conducted a field experiment that controlled three levels of deer densities (exclosure: 0 deer/km2, low: 10 deer/km2, and high: 20 deer/km2) and four anthropogenic disturbances (without anthropogenic disturbances [control], nitrogen addition, logging, and nitrogen addition and logging combined) in a cool temperate secondary forest in northern Japan for nine years. We surveyed the effects of deer density and anthropogenic disturbance treatments on species richness and vegetation cover of life forms (forbs, ferns, trees, graminoids, unpalatable species, vines, and shrubs) and all species of understory vascular plants. We estimated the constant effect (without the elapsed year) and the temporary effect (with the elapsed year) of deer density, anthropogenic disturbances, and their interactions on the species richness, vegetation cover, and Simpson’s index as separate parameters in full models and selected the best model. The high deer density negatively affected the species richness of some life forms and all species and accelerated these effects over time for all species. The vegetation covers of most of the life forms were negatively affected by high deer density, and the effect was reduced over time. In contrast, the exclosure negatively affected the species richness of some life forms and positively affected the vegetation cover of most of the life forms and all species. The effect on the cover accelerated over time. Nitrogen addition accelerated the negative effect of high deer density on the species richness of shrubs. On the other hand, logging reduced the negative effect of high deer density on the species richness of all species. The cover of unpalatable species in the high deer density site with logging was approximately nine times higher than that in the high deer density site without anthropogenic disturbances in the last surveyed year. The high deer density and logging decreased the Simpson’s diversity index score. These results indicate that the effects of deer density, anthropogenic disturbances, and their interactions vary with time. These interactions must be considered to manage deer’s effect on forest ecosystems.
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