The island of Crete, credited by some historical scholars as a central crucible of western civilization, has been under continuous archeological investigation since the second half of the nineteenth century. In the present work, the geographic stratification of the contemporary Cretan Y-chromosome gene pool was assessed by high-resolution haplotyping to investigate the potential imprints of past colonization episodes and the population substructure. In addition to analyzing the possible geographic origins of Y-chromosome lineages in relatively accessible areas of the island, this study includes samples from the isolated interior of the Lasithi Plateau - a mountain plain located in eastern Crete. The potential significance of the results from the latter region is underscored by the possibility that this region was used as a Minoan refugium. Comparisons of Y-haplogroup frequencies among three Cretan populations as well as with published data from additional Mediterranean locations revealed significant differences in the frequency distributions of Y-chromosome haplogroups within the island. The most outstanding differences were observed in haplogroups J2 and R1, with the predominance of haplogroup R lineages in the Lasithi Plateau and of haplogroup J lineages in the more accessible regions of the island. Y-STR-based analyses demonstrated the close affinity that R1a1 chromosomes from the Lasithi Plateau shared with those from the Balkans, but not with those from lowland eastern Crete. In contrast, Cretan R1b microsatellite-defined haplotypes displayed more resemblance to those from Northeast Italy than to those from Turkey and the Balkans.
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