Improved phylogenetic resolution for Y-chromosome Haplogroup O2a1c-002611

Xiaotian Yao,Beilei Bian,Chuan-Chao Wang,Gang Chen,Xiaoli Wu,Senwei Tang

doi:10.1038/s41598-017-01340-z

Xiaotian Yao, Beilei Bian + Show 4 more

Open Access

https://doi.org/10.1038/s41598-017-01340-z

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Abstract

Y-chromosome Haplogroup O2a1c-002611 is one of the dominant lineages of East Asians and Southeast Asians. However, its internal phylogeny remains insufficiently investigated. In this study, we genotyped 89 new highly informative single nucleotide polymorphisms (SNPs) in 305 individuals with Haplogroup O2a1c-002611 identified from 2139 Han Chinese males. Two major branches were identified, O2a1c1-F18 and O2a1c2-L133.2 and the first was further divided into two main subclades, O2a1c1a-F11 and O2a1c1b-F449, accounting for 11.13% and 2.20% of Han Chinese, respectively. In Haplogroup O2a1c1a-F11, we also determined seven sublineages with quite different frequency distributions in Han Chinese ranging from 0.187% to 3.553%, implying they might have different demographic history. The reconstructed haplogroup tree for all the major clades within Haplogroup O2a1c-002611 permits better resolution of male lineages in population studies of East Asia and Southeast Asia. The dataset generated in the present study are also valuable for forensic identification and paternity tests in China.

Highlights

The phylogeny of Y-chromosome provides a powerful tool to reconstruct genetic relationship of human populations and paternal lineages[1,2,3]
Among the 2139 male individuals, 305 of them (14.26%) belong to the O2a1c-002611 lineage (Table 1), in agreement with previous studies of East Asian populations[4, 12,13,14]. For these individuals with a derived allele at IMS-JST002611, we investigated other 88 single nucleotide polymorphisms (SNPs) purportedly belonging to the O2a1c-002611 haplogroup, and the results allowed us to update the phylogenetic tree of O2a1c-002611
The Haplogroup O2a1c1-F18 is further divided into two main subclades, O2a1c1a-F11 and O2a1c1b-F449, accounting for 11.13% and 2.20% of the Han Chinese, respectively

Summary

Introduction

The phylogeny of Y-chromosome provides a powerful tool to reconstruct genetic relationship of human populations and paternal lineages[1,2,3]. The Haplogroup O1a-M119, a sublineage of O1-M265, is prevalent along the southeast coast of China, occurring at high frequencies in Tai-Kadai speaking and Taiwan Austronesian-speaking people[8, 9]. Another sublineage of O1, O1b-M268, accounts for about 5% of the Han Chinese[4]. We describe a large-scale, nationwide study of Haplogroup O2a1c-002611 in Han Chinese by using high-density genotype data to examine phylogenetic positions of newly reported markers and provide useful tools for future population history analysis

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