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Hum Genet. 2018 Feb;137(2):161-173. doi: 10.1007/s00439-018-1869-0. Epub 2018 Jan 30.

Genomic structure of the native inhabitants of Peninsular Malaysia and North Borneo suggests complex human population history in Southeast Asia.

Author information

1
Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.
2
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.
3
Saw Swee Hock School of Public Health, National University of Singapore, 117597, Singapore, Singapore.
4
Faculty of Medicine, Institute of Medical Molecular Biotechnology, Universiti Teknologi MARA, Sungai Buloh Campus, 47000, Sg Buloh, Selangor, Malaysia.
5
Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, 46150, Sunway, Selangor, Malaysia.
6
Tropical Medicine and Biology Platform, Monash University Malaysia, Jalan Lagoon Selatan, 46150, Sunway, Selangor, Malaysia.
7
Faculty of Medicine and Health Sciences, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia.
8
Clinical Pathology Diagnostic Centre Research Laboratory, Faculty of Medicine, Universiti Teknologi MARA, Sungai Buloh Campus, 47000, Sg Buloh, Selangor, Malaysia.
9
Personal Genomics Institute, Genome Research Foundation, Suwon, Republic of Korea.
10
Geromics, Ulsan, 44919, Republic of Korea.
11
Biomedical Engineering Department, The Genomics Institute, UNIST, Ulsan, Republic of Korea.
12
School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
13
Collaborative Innovation Center of Genetics and Development, Shanghai, 200438, China.
14
NUS Graduate School for Integrative Science and Engineering, National University of Singapore, 117456, Singapore, Singapore.
15
Life Sciences Institute, National University of Singapore, Singapore, Singapore.
16
Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore.
17
Genome Institute of Singapore, Agency for Science, Technology and Research, 138672, Singapore, Singapore.
18
Biotechnology Research Institute, Universiti Malaysia Sabah, Jalan UMS, 88400, Kota Kinabalu, Sabah, Malaysia. vijay@ums.edu.my.
19
Faculty of Medicine and Health Sciences, UCSI University, Jalan Menara Gading, Taman Connaught, Cheras, 56000, Kuala Lumpur, Malaysia. hoh.boonpeng@gmail.com.

Abstract

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.

PMID:
29383489
DOI:
10.1007/s00439-018-1869-0

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