Scots pine is one of the most widely occurring pines, but future projections suggest a large reduction in its range, mostly at the southern European limits. A significant part of its range is located in the Caucasus, a global hot-spot of diversity. Pine forests are an important reservoir of biodiversity and endemism in this region. We explored demographic and biogeographical processes that shaped the genetic diversity of Scots pine in the Caucasus ecoregion and its probable future distribution under different climate scenarios. We found that the high genetic variability of the Caucasian populations mirrors a complex glacial and postglacial history that had a unique evolutionary trajectory compared to the main range in Europe. Scots pine currently grows under a broad spectrum of climatic conditions in the Caucasus, which implies high adaptive potential in the past. However, the current genetic resources of Scots pine are under high pressure from climate change. From our predictions, over 90% of the current distribution of Scots pine may be lost in this century. By threatening the stability of the forest ecosystems, this would dramatically affect the biodiversity of the Caucasus hot-spot.

Due to global climate cooling and aridification since the Paleogene, the members of the Neogene flora were extirpated from the Northern Hemisphere or were confined to a few refugial areas. For some species, the final reduction/extinction came in the Pleistocene, but some others have survived climatic transformations up to the present. This has occurred in Castanea sativa, a species of high commercial value in Europe and a significant component of the Caucasian forest biodiversity. In contrast to the European range, neither the historical biogeography nor the population genetic structure of the species in the isolated Caucasian range has been clarified. Here, based on a survey of 21 natural populations from the Caucasus and a single one from Europe, we provide likely biogeographic reconstruction and genetic diversity details. By applying Bayesian inference, species distribution modelling, and fossil pollen data, we estimated (1) the time of the Caucasian - European divergence during the Middle Pleistocene (436.5 ka), (2) the time of divergence among Caucasian lineages, and (3) outlined the glacial refugia for species. The climate changes related to the Early Middle Pleistocene Transition and the alpine orogenic uplift in the region are proposed as the major drivers of the intraspecific divergence and European-Caucasian disjunction, while the impact of the last glacial cycle was of marginal importance.