Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society (CAS-MPG) Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
Hum Genet. 2014 Sep;133(9):1169-85. doi: 10.1007/s00439-014-1459-8. Epub 2014 Jun 11.
Peninsular Malaysia is a strategic region which might have played an important role in the initial peopling and subsequent human migrations in Asia. However, the genetic diversity and history of human populations--especially indigenous populations--inhabiting this area remain poorly understood. Here, we conducted a genome-wide study using over 900,000 single nucleotide polymorphisms (SNPs) in four major Malaysian ethnic groups (MEGs; Malay, Proto-Malay, Senoi and Negrito), and made comparisons of 17 world-wide populations. Our data revealed that Peninsular Malaysia has greater genetic diversity corresponding to its role as a contact zone of both early and recent human migrations in Asia. However, each single Orang Asli (indigenous) group was less diverse with a smaller effective population size (N(e)) than a European or an East Asian population, indicating a substantial isolation of some duration for these groups. All four MEGs were genetically more similar to Asian populations than to other continental groups, and the divergence time between MEGs and East Asian populations (12,000--6,000 years ago) was also much shorter than that between East Asians and Europeans. Thus, Malaysian Orang Asli groups, despite their significantly different features, may share a common origin with the other Asian groups. Nevertheless, we identified traces of recent gene flow from non-Asians to MEGs. Finally, natural selection signatures were detected in a batch of genes associated with immune response, human height, skin pigmentation, hair and facial morphology and blood pressure in MEGs. Notable examples include SYN3 which is associated with human height in all Orang Asli groups, a height-related gene (PNPT1) and two blood pressure-related genes (CDH13 and PAX5) in Negritos. We conclude that a long isolation period, subsequent gene flow and local adaptations have jointly shaped the genetic architectures of MEGs, and this study provides insight into the peopling and human migration history in Southeast Asia.
马来半岛是一个战略区域，它可能在亚洲人类的初始迁徙和随后的人类迁徙中发挥了重要作用。然而，该地区人口（尤其是原住民）的遗传多样性和历史仍知之甚少。在这里，我们使用超过 90 万个单核苷酸多态性（SNP）对四个主要马来西亚族群（马来人、原始马来人、塞诺伊人和尼格利陀人）进行了全基因组研究，并与 17 个世界范围的人群进行了比较。我们的数据表明，马来半岛拥有更大的遗传多样性，这与其作为亚洲早期和近期人类迁徙的交汇区的角色相对应。然而，每个原始马来族群（原住民）的多样性都比欧洲或东亚人群要小，有效种群规模（N(e)）也更小，这表明这些群体经历了相当长一段时间的隔离。这四个马来西亚族群在遗传上与亚洲人群更为相似，而与其他大陆群体的差异则更小，它们与东亚人群的分化时间（12000-6000 年前）也比东亚人群与欧洲人群的分化时间（45000-6000 年前）短得多。因此，尽管马来西亚的原住民群体特征明显不同，但它们可能与其他亚洲群体有着共同的起源。然而，我们也发现了非亚洲人群向马来西亚族群输入基因的痕迹。最后，我们在一批与免疫反应、人类身高、皮肤色素沉着、头发和面部形态以及血压相关的基因中检测到了自然选择的迹象。值得注意的例子包括与所有原始马来族群的人类身高相关的 SYN3、一个与身高相关的基因（PNPT1）和两个与血压相关的基因（CDH13 和 PAX5）在尼格利陀人中。我们的结论是，长时间的隔离、随后的基因流动和局部适应共同塑造了马来西亚族群的遗传结构，这项研究为东南亚的人类迁徙和人类迁徙历史提供了新的认识。
