Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.
Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, Shanghai, China.
Hum Genet. 2018 Feb;137(2):161-173. doi: 10.1007/s00439-018-1869-0. Epub 2018 Jan 30.
Southeast Asia (SEA) is enriched with a complex history of peopling. Malaysia, which is located at the crossroads of SEA, has been recognized as one of the hubs for early human migration. To unravel the genomic complexity of the native inhabitants of Malaysia, we sequenced 12 samples from 3 indigenous populations from Peninsular Malaysia and 4 native populations from North Borneo to a high coverage of 28-37×. We showed that the Negritos from Peninsular Malaysia shared a common ancestor with the East Asians, but exhibited some level of gene flow from South Asia, while the North Borneo populations exhibited closer genetic affinity towards East Asians than the Malays. The analysis of time of divergence suggested that ancestors of Negrito were the earliest settlers in the Malay Peninsula, whom first separated from the Papuans ~ 50-33 thousand years ago (kya), followed by East Asian (~ 40-15 kya), while the divergence time frame between North Borneo and East Asia populations predates the Austronesian expansion period implies a possible pre-Neolithic colonization. Substantial Neanderthal ancestry was confirmed in our genomes, as was observed in other East Asians. However, no significant difference was observed, in terms of the proportion of Denisovan gene flow into these native inhabitants from Malaysia. Judging from the similar amount of introgression in the Southeast Asians and East Asians, our findings suggest that the Denisovan gene flow may have occurred before the divergence of these populations and that the shared similarities are likely an ancestral component.
东南亚（SEA）拥有丰富的人类迁徙历史。马来西亚位于东南亚的十字路口，被认为是早期人类迁徙的中心之一。为了解开马来西亚本地居民的基因组复杂性之谜，我们对来自马来半岛的 3 个原住民群体和来自北婆罗洲的 4 个原住民群体的 12 个样本进行了测序，覆盖率高达 28-37×。结果表明，来自马来半岛的尼格利陀人与东亚人有共同的祖先，但也存在一定程度的来自南亚的基因流，而北婆罗洲的群体与东亚人比与马来人更具遗传亲和力。分化时间分析表明，尼格利陀人的祖先最早是马来半岛的定居者，他们与巴布亚人在 5 万至 3.3 万年前（kya）首次分离，其次是东亚人（~40-15 kya），而北婆罗洲和东亚人群之间的分化时间框架早于南岛语系的扩张期，这表明可能存在新石器时代前的殖民化。我们的基因组证实了大量的尼安德特人遗传背景，这在其他东亚人中也有观察到。然而，在这些马来西亚本地居民中，从尼安德特人基因流入的比例方面并没有观察到显著差异。从东南亚人和东亚人中相似的基因渗入量来看，我们的发现表明，这种尼安德特人基因流可能发生在这些群体分化之前，而这些群体之间的相似之处可能是一个祖先成分。
