Human activities have altered the composition of biotas through two fundamental processes: native extinctions and alien introductions. Both processes affect the taxonomic (i.e., species identity) and phylogenetic (i.e., species evolutionary history) structure of species assemblages. However, it is not known what the relative magnitude of these effects is at large spatial scales. Here we analyze the large-scale effects of plant extinctions and introductions on taxonomic and phylogenetic diversity of floras across Europe, using data from 23 regions. Considering both native losses and alien additions in concert reveals that plant invasions since AD 1500 exceeded extinctions, resulting in (i) increased taxonomic diversity (i.e., species richness) but decreased phylogenetic diversity within European regions, and (ii) increased taxonomic and phylogenetic similarity among European regions. Those extinct species were phylogenetically and taxonomically unique and typical of individual regions, and extinctions usually were not continent-wide and therefore led to differentiation. By contrast, because introduced alien species tended to be closely related to native species, the floristic differentiation due to species extinction was lessened by taxonomic and phylogenetic homogenization effects. This was especially due to species that are alien to a region but native to other parts of Europe. As a result, floras of many European regions have partly lost and will continue to lose their uniqueness. The results suggest that biodiversity needs to be assessed in terms of both species taxonomic and phylogenetic identity, but the latter is rarely used as a metric of the biodiversity dynamics.
