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显著的族群组成——本州人群（Hondo）、琉球人群（Ryukyu）与阿伊努人群（Ainu）。通过主成分分析（principal-component analysis），尽管这三个族群可被清晰区分，但占日本总人口99%的本州人群却形成了一个几乎无法区分的聚类簇。为解析精细尺度的遗传结构，我们采用基于单体型（haplotype）的高效统计方法，对来自日本8个不同区域的1600名日本个体的全基因组单核苷酸多态性（single nucleotide polymorphism, SNP）数据进行分析。随后，我们将日本人群数据与另外26个亚洲人群的数据进行整合，以分析其共享祖先成分与遗传分化情况。本研究发现，在本数据集内日本人群可被划分为9个遗传聚类簇，其分布与地理区域呈现显著一致性；且日本人群的祖先成分主要源自朝鲜人群与汉族人群聚类簇。我们还检测并估算了日本人群的混血事件发生时间。尽管琉球人群与本州人群之间的遗传分化部分由正选择（positive selection）所导致，但本州人群各聚类簇间的遗传分化主要源自遗传漂变（genetic drift）。值得注意的是，在亚洲人群中，我们发现正选择可能会加剧远缘人群间的遗传分化，而削弱近缘人群间的遗传分化。上述研究发现对人类演化与医学遗传学研究具有重要意义。