Ancient DNAs and the Neolithic Chinese super-grandfather Y haplotypes

Abstract Background: Previous studies identified 3 Neolithic Han Chinese super-grandfather Y haplotypes, F5 (O2a2b1a1a), F46 (O2a2b1a2a1), and F11 (O2a1b1a1a1a), but their relationships with the archaeological and written records remain unexplored. Results: We here report genome wide DNA data for 11 ancient human samples (0.02x-1.28x) from China ranging from 6500 to 2500 years before present (YBP), which also includes ~11 Mb Y NRY data for one sample. The 11 ancient samples belonged to 4 different genetic groups, designated as Dashanqian (DSQ) of Xiajiadian Culture in the Northeast, Duzhong (DZ) of late Yangshao Culture in the Central Plains, Zhengzhou Xishan (ZX) of Miaodigou Culture in the Central Plains, and Others. Present day F5 samples were closer in autosomal distances to the ZX and DSQ groups while O1, O2, and C samples were closer to the DZ group. We also sequenced the Y chromosome of one of these ancient samples K12 from DSQ and found both K12 and a previously reported ~4000 year old sample MG48 from Northwest China to have the F2137 (O2a2b1a1a1a2a) haplotype, belonging to the most prolific branch F438 immediately under F5. We further found close relationships between ZX and DSQ and between ZX and ancient M117 Tibetans or present day Southwest Dai Chinese carrying the F5 subtype O2a2b1a1a6. Conclusions: The results imply radiations of F5 subtypes from the putative place of F5 origin in Henan. These results are remarkably consistent with archaeological and written records.