An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4

Abstract

Y-chromosome Haplogroup O is the dominant lineage of East Asians, comprising more than a quarter of all males on the world; however, its internal phylogeny remains insufficiently investigated. In this study, we determined the phylogenetic position of recently defined markers (L127, KL1, KL2, P164, and PK4) in the background of Haplogroup O. In the revised tree, subgroup O3a-M324 is divided into two main subclades, O3a1-L127 and O3a2-P201, covering about 20 and 35% of Han Chinese people, respectively. The marker P164 is corrected from a downstream site of M7 to upstream of M134 and parallel to M7 and M159. The marker PK4 is also relocated from downstream of M88 to upstream of M95, separating the former O2(*) into two parts. This revision evidently improved the resolving power of Y-chromosome phylogeny in East Asia.

Figure 1

The updated tree of Haplogroup O and the frequencies of its subgroups in Han Chinese population. The newly located SNPs and renamed lineages are labeled in bold. Samples with derived allele of M164 from our previous studies were typed at L127, KL1, and KL2 in order to locate it in the revised tree. ‘East' refers to the samples whose origins are from the provinces of Jiangsu, Anhui, Zhejiang, and Shanghai, whereas ‘North' and ‘South' refers to the other provinces of which the capitals locate northern or southern to the Line of Qinling Mountains-Huai River, respectively. The samples typed besides Haplogroup O include C-M130 (27, 7.5%), D-M174 (7, 1.9%), G-M201 (1, 0.3%), N-M231 (18, 5.0%), Q-M242 (12, 3.3%), and R-M207 (4, 1.1%).