Ten populations of Caucasian juniper J. communis var. oblonga were analyzed using seven microsatellite nSSR loci to draw conclusions about migration routes and genetic relationships with populations in the northern part of their range. These new data were combined with data previously obtained from the main Eurasian range. The results of nSSR analysis confirm the data on the cpDNA structure of J. communis var. oblonga about the existence of a deep divergence between the populations of the eastern part of the Greater Caucasus and the populations of the main range, which is likely due to the long-term isolation of juniper in this part of the Caucasus. At the same time, the results indicate the existence of a juniper gene flow from the main range towards the Western Caucasus, which was more intense with seeds. The migration routes of birds established during interglacial periods contributed to the dispersal of seeds over long distances and contacts of juniper from the main part of its range with juniper in the western part of the Caucasus, which was reflected in the structure of nuclear DNA.
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