The total of 257 trees from the ten natural Siberian stone pine populations of West Siberian Plain, Ural Mountains and Kuznetsk Alatau were studied with the eight nuclear microsatellite loci. Differentiation of population groups indicates the possible existence of separate refugia in the past in the Urals and Kuznetsk Alatau. The northern populations of Western Siberia were characterized by a reduced level of genetic diversity, which could be a consequence of the founder effect in the process of P. sibirica migration from the southern regions of Western Siberia and the Urals since the end of the last glacial maximum. The genetic variability distribution among populations shows the uneven dynamics of Siberian stone pine migration from the zones of supposed refugia. The map of the proposed ways of Siberian stone pine migration from the zones of possible refugia was constructed, and it is in a good agreement with the results of palynological investigations.

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