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Y chromosome evidence of earliest modern human settlement in East Asia and multiple origins of Tibetan and Japanese populations

Hong Shi1, Hua Zhong2, Yi Peng1, Yong-Li Dong3, Xue-Bin Qi1, Feng Zhang4, Lu-Fang Liu5, Si-Jie Tan3, Runlin Z Ma2, Chun-Jie Xiao3, R Spencer Wells6, Li Jin4 and Bing Su1*

Author Affiliations

1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology and Kunming Primate Research Centre, Chinese Academy of Sciences, Kunming, PR China

2 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, PR China

3 Human Genetics Centre, Yunnan University, Kunming, PR China

4 State Key Laboratory of Genetic Engineering and Center for Anthropological Studies, School of Life Sciences, Fudan University, Shanghai, PR China

5 Huaihua Medical College, Huaihua, Hunan, PR China

6 The Genographic Project, National Geographic Society, Washington, USA

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BMC Biology 2008, 6:45  doi:10.1186/1741-7007-6-45

Published: 29 October 2008



The phylogeography of the Y chromosome in Asia previously suggested that modern humans of African origin initially settled in mainland southern East Asia, and about 25,000–30,000 years ago, migrated northward, spreading throughout East Asia. However, the fragmented distribution of one East Asian specific Y chromosome lineage (D-M174), which is found at high frequencies only in Tibet, Japan and the Andaman Islands, is inconsistent with this scenario.


In this study, we collected more than 5,000 male samples from 73 East Asian populations and reconstructed the phylogeography of the D-M174 lineage. Our results suggest that D-M174 represents an extremely ancient lineage of modern humans in East Asia, and a deep divergence was observed between northern and southern populations.


We proposed that D-M174 has a southern origin and its northward expansion occurred about 60,000 years ago, predating the northward migration of other major East Asian lineages. The Neolithic expansion of Han culture and the last glacial maximum are likely the key factors leading to the current relic distribution of D-M174 in East Asia. The Tibetan and Japanese populations are the admixture of two ancient populations represented by two major East Asian specific Y chromosome lineages, the O and D haplogroups.