Background: At the southern entrance to East Asia, early population migration has affected most of the Y-chromosome variations of East Asians.
Methodology/principal findings: To assess the isolated genetic structure of Hainan Island and the original genetic structure at the southern entrance, we studied the Y chromosome diversity of 405 Hainan Island aborigines from all the six populations, who have little influence of the recent mainland population relocations and admixtures. Here we report that haplogroups O1a* and O2a* are dominant among Hainan aborigines. In addition, the frequency of the mainland dominant haplogroup O3 is quite low among these aborigines, indicating that they have lived rather isolated. Clustering analyses suggests that the Hainan aborigines have been segregated since about 20 thousand years ago, after two dominant haplogroups entered East Asia (31 to 36 thousand years ago).
Conclusions/significance: Our results suggest that Hainan aborigines have been isolated at the entrance to East Asia for about 20 thousand years, whose distinctive genetic characteristics could be used as important controls in many population genetic studies.