A new paper has revised some details of the phylogeny of Y-DNA haplogroup O, specially of O3:
Shi Yan et al., An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4. European Journal of Human Genetics, 2011. Pay per view. [doi: 10.1038/ejhg.2011.64]
A copy of the paper can be read (for a year) here.
Most importantly, three subclades (O3a1, O3a2 and O3a4 prior to this review) have been joined in a single subclade of O3a that gets the name O3a1, defined by newly described mutations L127, KL1 and KL2.
Former O3a3, the most common lineage in China, is now relabeled O3a2 (per the paper’s proposal) and subclade O3a3b2 (P164) goes up in the hierarchy as O3a2c, absorbing its “uncle” (O3a3c – M134) as a subclade (now O3a2c1) and becoming independent from its former “father” lineage O3a3b (M7), which retains the name.
Another subclade moved up in the phylogenetic hierarchy is former O2a1a (PK4), which is now revealed to be ancestral (and not descendant) to former O2a (M95).
Figure 1 should help understanding these changes:
|click to expand|
The three regions (East, North, South) refer to regions of China (rough references: Shanghai, Beijing and Guangzhou respectively, I guess). Most haplogroups are quite evenly distributed but some are only (or almost only) found in the South. These are (by the new nomenclature): O1a2, O2a*, O2b and O3a2a. Inversely O3a1a is not found in the South (dominant in the East instead). Notice that because of the samples being taken from students at a Shanghai university, East China is oversampled.
A discussion in Chinese can be found also in this Forum of Molecular Anthropology. Thanks to Natsuya for the info.