Acknowledgments: Author contributions DT and AG analyzed the data and wrote the text. MM coordinated molecular genetic work and provided primary data analysis; MG did much of genetic analysis and identification of the haplogroups; GT initiated human genetic studies at Ilia State University, discussed the results from the standpoint of history and social sciences, and made much effort to provide the research with all necessary resources. Y-DNA haplogroup diversity is most commonly used for the analysis of the ancestry of individual ethnic groups or linguistic families (Kayser et al. 1997;Brisighelli, 2012). The reason is that Y-DNA haplogroups generally show more distinct ethno-geographic patterns than matrilineally inherited mt-DNA (Comas et al. 2000;Nasidze et al. 2003Nasidze et al. , 2004b. This is most likely due to higher dispersal rates of women (Seielstad et al. 1998;Oota et al. 2001;Nasidze et al. 2004a), the effects of selective pressures on the mitochondrial genome (Mishmar et al. 2003) and/or sex ratio in favor of women, causing more genetic drift in males (Dupanloup et al. 2003). Moreover, there is a popular nomenclature of the haplogroups linked to a well-established phylogenetic pattern (Underhill et al. 2001;Y Chromosome Consortium, 2002;Karafet et al. 2008;Chiaroni et al. 2009).The Caucasus is among the most linguistically and culturally diverse regions of Eurasia (Comrie, 2008;Nasidze et al. 2004b;Marchani et al. 2008;Balanovsky et al. 2011;Yunusbayev et al. 2012). Currently, the region hosts dozens of languages that are grouped into three language families (Comrie, 2008):Caucasian, Indo-European and Turkic. The Caucasian language family traditionally includes Adyghean, Vainakh, Daghestanian, and Kartvelian languages (Catford, 1977), although the common origin of these languages is disputed (Starostin, 1989). Recent study by Pagel et al. (2013) shows that the Kartvelian and Dravidic language families are the most basal in relation to the other Eurasian language families. Diakonoff and Starostin (1988) suggest that Vainakh and Daghestanian (i.e. Northeast Caucasian languages) are related to extinct Hurro-Urartian. Armenian and Ossetian languages belong to the IndoEuropean language family, and Oghuz and Kypchak subgroups of the Turkic language group are spoken in the Caucasus as well (Catford, 1977;Comrie, 2008). Linguistic differences, along with the differences in political history, influence (but do not determine) the ethnic identities of the people inhabiting the region. Some ethnic boundaries (e.g. that of Armenians or Ossetians) coincide with the linguistic boundaries but those of the other ethnic groups only partly do so. Some groups speaking several mutually unintelligible but related languages consider themselves to be part of a single ethnos -e.g. Georgians or Avarians.Simultaneously, language rather than religion accounts for ethnic identity in the Caucasus -e.g. Ossetians, Abkhazians and Georgians maintain ethnic integrity in spite of different religions practiced within each of these ...