The average Gst value for all markers in the three South Caucasus groups was 0.010. It is half as much as that for European populations (0.018) [16] and it is significantly lower than Gst obtained for mountain inhabitants of Dagestan (0.045) [18]. The Gst calculated for the Dagestan populations is based on the same markers that we used in this study. In spite of the absence in our study of three Alu loci used by Yunusbayev et al. [18] (NBC51, B65, A25), the difference in genetic differentiation between the South Caucasus and Dagestan populations is obvious. It was shown that pure drift was not the sole reason for such differentiation in Dagestan and could possibly be the result of migrations and isolation in steppe and mountain populations, respectively. Thus, the possible reason for the difference in the Gst value is that the isolation in Abkhazian settlements is not as strong as it is in Dagestan, where an aul (a remote mountain village) can be considered as an isolate [20]. Furthermore, the populations studied do not represent the aul inhabitants. The main reason for the expected genetic differences in Abkhazian populations, which can be seen on the PC plot, could be historical and genetic distinction. The Mingrelians are the descendants of Georgian tribes, which inhabited the central region and foothills of Colchis on the territory of present-day western Georgia and Abkhazia. Due to centuries-old neighborhoods and contacts with western Georgian ethnic groups, the Abkhazians gained common anthropological and cultural traits from them. Although anthropologically Abkhazians are most close to western Georgian groups, which are intermediate between Pontic and Armenoid types (while signs of Caucasian type are not expressed), Abkhazians are more culturally and linguistically close to North-Caucasian Adygs. The Indo-European speaking Armenians are quite different from our two other groups, both linguistically and anthropologically. Yet the genetic difference between them and the two other groups (0.007) is slightly lower than that between the Abkhazian and Georgian populations (0.009). The main reason for this could be the penetration of Kartvel and Abkhaz-Adyghe elements to the Armenian gene pool because of dispersal settling of different Armenian groups in the Caucasus.

      Although classical markers (blood groups, serum proteins and red cell enzymes) showed clinal frequency distribution from Anatolia to Europe, later studies did not show any such signs [21]. In a previous study [4], it was shown that Alu insertion analyses along with mtDNA data places the Caucasus populations alongside European populations. It was proposed then that the Caucasus populations represent an earlier “layer” of the European populations [22]. That European and Caucasus populations are close to each other has now been confirmed [17].

      Our principal component analysis clearly distinguishes the populations of the Caucasus and Asia. However, we cannot exclude a Neolithic contribution to the contemporary gene pool. The possible reason for the absence of the frequency distribution gradient can be genetic drift, reinforced by isolation that could conceal the influence of Neolithic farmers on the Caucasus populations [1,21]. Our study can neither confirm nor disprove both these assumptions. Markers with high powers of resolution should be used to determine the extent of impact on the Caucasus populations from the Near East.          

       In summary, our analysis of eight Alu loci in three South Caucasian groups revealed a close relationship between them. The geographic neighborhood showed significant influence on genetic proximity in spite of linguistic and cultural differences between the groups. Our results confirm that geographic differentiation correlate with genetic diversity to a greater degree than linguistic differentiation. While an Alu insertion marker does not have enough power of resolution to assess the contribution of the influence of Neolithic farmers on the Caucasian gene pool, it clearly separates both South and North Caucasus populations (except Karanogays) from Siberian and Asian populations.