Jun Wang1,2,3,4,12, Wei Wang1,3,12, Ruiqiang Li1,3,4,12, Yingrui Li1,5,6,12, Geng Tian1,7, Laurie Goodman1, Wei Fan1, Junqing Zhang1, Jun Li1, Juanbin Zhang1, Yiran Guo1,7, Binxiao Feng1, Heng Li1,8, Yao Lu1, Xiaodong Fang1, Huiqing Liang1, Zhenglin Du1, Dong Li1, Yiqing Zhao1,7, Yujie Hu1,7, Zhenzhen Yang1, Hancheng Zheng1, Ines Hellmann9, Michael Inouye8, John Pool9, Xin Yi1,7, Jing Zhao1, Jinjie Duan1, Yan Zhou1, Junjie Qin1,7, Lijia Ma1,7, Guoqing Li1, Zhentao Yang1, Guojie Zhang1,7, Bin Yang1, Chang Yu1, Fang Liang1,7, Wenjie Li1, Shaochuan Li1, Dawei Li1, Peixiang Ni1, Jue Ruan1,7, Qibin Li1,7, Hongmei Zhu1, Dongyuan Liu1, Zhike Lu1, Ning Li1,7, Guangwu Guo1,7, Jianguo Zhang1, Jia Ye1, Lin Fang1, Qin Hao1,7, Quan Chen1,5, Yu Liang1,7, Yeyang Su1,7, A. san1,7, Cuo Ping1,7, Shuang Yang1, Fang Chen1,7, Li Li1, Ke Zhou1, Hongkun Zheng1,4, Yuanyuan Ren1, Ling Yang1, Yang Gao1,6, Guohua Yang1,2, Zhuo Li1, Xiaoli Feng1, Karsten Kristiansen4, Gane Ka-Shu Wong1,10, Rasmus Nielsen9, Richard Durbin8, Lars Bolund1,11, Xiuqing Zhang1,6, Songgang Li1,2,5, Huanming Yang1,2,3 & Jian Wang1,2,3

Here we present the first diploid genome sequence of an Asian individual. The genome was sequenced to 36-fold average coverage using massively parallel sequencing technology. We aligned the short reads onto the NCBI human reference genome to 99.97% coverage, and guided by the reference genome, we used uniquely mapped reads to assemble a high-quality consensus sequence for 92% of the Asian individual’s genome. We identified approximately 3 million single-nucleotide polymorphisms (SNPs) inside this region, of which 13.6% were not in the dbSNP database. Genotyping analysis showed that SNP identification had high accuracy and consistency, indicating the high sequence quality of this assembly. We also carried out heterozygote phasing and haplotype prediction against HapMap CHB and JPT haplotypes (Chinese and Japanese, respectively), sequence comparison with the two available individual genomes (J. D. Watson and J. C. Venter), and structural variation identification. These variations were considered for their potential biological impact. Our sequence data and analyses demonstrate the potential usefulness of next-generation sequencing technologies for personal genomics.

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Shi H, Zhong H, Peng Y, Dong YL, Qi XB, Zhang F, Liu LF, Tan SJ, Ma RL, Xiao CJ, Wells S, Jin L, Su B.
ABSTRACT: BACKGROUND: The phylogeography of the Y chromosome in Asia previously suggested that modern humans of African origin initially settled in mainland southern East Asia, and about 25,000-30,000 years ago, migrated northward, spreading throughout East Asia. However, the fragmented distribution of one East Asian specific Y chromosome lineage (D-M174), which is found at high frequencies only in Tibet, Japan and the Andaman Islands, is inconsistent with this scenario. RESULTS: In this study, we collected more than 5,000 male samples from 73 East Asian populations and reconstructed the phylogeography of the D-M174 lineage. Our results suggest that D-M174 represents an extremely ancient lineage of modern humans in East Asia, and a deep divergence was observed between northern and southern populations. CONCLUSIONS: We proposed that D-M174 has a southern origin and its northward expansion occurred about 60,000 years ago, predating the northward migration of other major East Asian lineages. The Neolithic expansion of Han culture and the last glacial maximum are likely the key factors leading to the current relic distribution of D-M174 in East Asia. The Tibetan and Japanese populations are the admixture of two ancient populations represented by two major East Asian specific Y chromosome lineages, the O and D haplogroups

摘要： 来自中科院昆明动物研究所消息，以前的遗传学研究表明，东亚现代人起源于非洲并最早到达东亚大陆的南方。而后，在大约25000－30000年前左右，出现了一次大规模的由南向北的人群迁徙，从而使现代人遍布东亚大陆。

来自中科院昆明动物研究所消息，以前的遗传学研究表明，东亚现代人起源于非洲并最早到达东亚大陆的南方。而后，在大约25000－30000年前左右，出现了一次大规模的由南向北的人群迁徙，从而使现代人遍布东亚大陆。

然而，东亚人群的Y染色体单倍型中存在一种东亚特有，但分布奇特的单倍型－D174单倍型（又称YAP单倍型）。它在中国的藏族、日本人和东南亚阿德曼群岛人群中有很高的频率（>30%），但在其他东亚人群中频率很低。

宿兵实验室（助理研究员石宏）最近对D174单倍型进行了系统的研究，发现它实际上代表了一个非常古老的东亚现代人的Y染色体单倍型。经过对73个东亚代表人群的分析，他们认为D174单倍型起源于东亚的南部，且其由南向北的迁徙大约发生在距今6万年前，远远早于发生在25000－30000年左右的那次大迁徙，可能是发生在东亚大陆最早的大规模现代人群的迁徙。由于最近一次冰河期的恶劣气候以及新石器时代(10000年前)以来华夏文明的扩散，现在的东亚人群中只有少数人群保存了那次史前迁徙的遗传印记。

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