The fine-scale genetic structure and evolution of the Japanese population

The contemporary Japanese populations largely consist of three genetically distinct groups—Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics.

当代日本人群体主要由三个遗传分化明确的群体构成——本州（Hondo）、琉球（Ryukyu）与阿伊努（Ainu）。通过主成分分析（principal-component analysis），尽管这三个群体可被清晰区分，但占日本总人口99%的本州人群形成了一个几乎难以区分的聚类。为解析精细尺度的遗传结构，我们将基于单倍型的高功效统计方法应用于来自日本8个不同区域的1600名个体的全基因组单核苷酸多态性（single nucleotide polymorphism, SNP）数据。随后我们将日本人群数据与另外26个亚洲人群的数据合并，以分析共同祖先关系与遗传分化。我们发现，本数据集可将日本人群划分为九个遗传聚类，其分布与地理格局呈现显著一致性；且日本人群的祖先遗传背景主要源自朝鲜半岛与汉族聚类。我们还检测到日本人群的基因混合事件并确定了其发生时间。研究表明，琉球与本州人群间的遗传分化部分由正向选择（positive selection）所致，而本州人群内部各聚类间的遗传分化则主要源于遗传漂变（genetic drift）。值得注意的是，在亚洲人群中，我们发现正向选择可能会加剧远距离人群间的遗传分化，却削弱近距离人群间的遗传分化。这些研究发现对于人类演化与医学遗传学研究具有重要意义。