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Tracing the legacy of the early Hainan Islanders - a perspective from mitochondrial DNA

Min-Sheng Peng135, Jun-Dong He123, Hai-Xin Liu126 and Ya-Ping Zhang134*

Author affiliations

1 State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, P.R. China

2 School of Life Science, University of Science and Technology of China, Hefei, P.R. China

3 KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, P.R. China

4 Laboratory for Conservation and Utilization of Bio-resources, Yunnan University, Kunming, P.R. China

5 Graduate School of the Chinese Academy of Sciences, Beijing, P.R. China

6 Current address: Program in Neuroscience, SUNY at Stony Brook, Stony Brook, New York, USA

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Citation and License

BMC Evolutionary Biology 2011, 11:46  doi:10.1186/1471-2148-11-46

Published: 15 February 2011



Hainan Island is located around the conjunction of East Asia and Southeast Asia, and during the Last Glacial Maximum (LGM) was connected with the mainland. This provided an opportunity for the colonization of Hainan Island by modern human in the Upper Pleistocene. Whether the ancient dispersal left any footprints in the contemporary gene pool of Hainan islanders is debatable.


We collected samples from 285 Li individuals and analyzed mitochondrial DNA (mtDNA) variations of hypervariable sequence I and II (HVS-I and II), as well as partial coding regions. By incorporating previously reported data, the phylogeny of Hainan islanders was reconstructed. We found that Hainan islanders showed a close relationship with the populations in mainland southern China, especially from Guangxi. Haplotype sharing analyses suggested that the recent gene flow from the mainland might play important roles in shaping the maternal pool of Hainan islanders. More importantly, haplogroups M12, M7e, and M7c1* might represent the genetic relics of the ancient population that populated this region; thus, 14 representative complete mtDNA genomes were further sequenced.


The detailed phylogeographic analyses of haplogroups M12, M7e, and M7c1* indicated that the early peopling of Hainan Island by modern human could be traced back to the early Holocene and/or even the late Upper Pleistocene, around 7 - 27 kya. These results correspond to both Y-chromosome and archaeological studies.