I haven't read this yet, but it looks like an intriguing paper. It's probably a sign of things to come, not only for the origins of the Han Chinese but many populations generally thought to be genetically homogenous. Note also how each of the identified haplogroups (N, O*, O2a, O3a, and Q1a1) appear to be associated with specific burial customs and inferred social status. Fascinating stuff.
Objectives: Y chromosome haplogroup Q1a1 is found almost only in Han Chinese populations. However, it has not been found in ancient Han Chinese samples until now. Thus, the origin of haplogroup Q1a1 in Han Chinese is still obscure. This study attempts to provide answer to this question, and to uncover the origin and paternal genetic structure of the ancestors of the Han Chinese.
Methods: Eighty-nine ancient human remains that were excavated from the presumed geographic source of the Han Chinese and dated to approximately 3,000 years ago were treated by the amelogenin gene polymerase chain reaction test, to determine their sex. Then, Y chromosome single nucleotide polymorphisms were subsequently analyzed from the samples detected as male.
Results: Samples from 27 individuals were successfully amplified. Their haplotypes could be attributed to haplogroups N, O*, O2a, O3a, and Q1a1. Analyses showed that the assigned haplogroup of each sample is correlated to the suspected social status and observed burial custom associated with the sample.
Conclusions: The origins of the observed haplotypes and their distribution in present day Han Chinese and in the samples suggest that haplogroup Q1a1 was probably introduced into the Han Chinese population approximately 3,000 years ago.
It'll be interesting to learn about the genome-wide genetic structure of the population that introduced haplogroup Q1a1 into the ancestral Han gene pool. Were they perhaps in large part Ancient North Eurasian (ANE)? The reason I say this is because Q is the most common Y-chromosome haplogroup in the Americas, where ANE peaks today. It's also the sister clade of haplogroup R, which is the paternal marker of Mal'ta boy, or the MA-1 genome, the main reference sample for ANE.
Yong-Bin Zhao etal., Ancient DNA evidence reveals that the Y chromosome haplogroup Q1a1 admixed into the Han Chinese 3,000 years ago, American Journal of Human Biology, Article first published online: 18 AUG 2014, DOI: 10.1002/ajhb.22604
First genome of an Upper Paleolithic human (Mal'ta boy)
Ancient European admixture in the Americas, or ancient Amerindian admixture in Europe?
Ancient human genomes suggest (more than) three ancestral populations for present-day Europeans