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Sci Rep. 2015 Sep 23;5:14375. doi: 10.1038/srep14375.

Dissecting the genetic structure and admixture of four geographical Malay populations.

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Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
Faculty of Medicine and Health Sciences, UCSI University, Jalan Merana Gading, Taman Connought, 56000, Kuala Lumpur, Malaysia.
Saw Swee Hock School of Public Health, National University of Singapore, Singapore.
Life Sciences Institute, National University of Singapore, Singapore.
Department of Public Health, Faculty of Medicine, University of Kelaniya, Ragama 11010, Sri Lanka.
Department of Medicine, Faculty of Medicine, University of Kelaniya, Ragama 11010, Sri Lanka.
Department of Pediatrics, School of Medical Sciences, Universiti Sains Malaysia, Kelantan 16150, Malaysia.
Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo 1628655, Japan.
NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore.
Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.
Department of Statistics and Applied Probability, National University of Singapore, Singapore.
School of Life Science and Technology, ShanghaiTec University, Shanghai 200031, China.
Collaborative Innovation Center of Genetics and Development, Shanghai 200438, China.


The Malay people are an important ethnic composition in Southeast Asia, but their genetic make-up and population structure remain poorly studied. Here we conducted a genome-wide study of four geographical Malay populations: Peninsular Malaysian Malay (PMM), Singaporean Malay (SGM), Indonesian Malay (IDM) and Sri Lankan Malay (SLM). All the four Malay populations showed substantial admixture with multiple ancestries. We identified four major ancestral components in Malay populations: Austronesian (17%-62%), Proto-Malay (15%-31%), East Asian (4%-16%) and South Asian (3%-34%). Approximately 34% of the genetic makeup of SLM is of South Asian ancestry, resulting in its distinct genetic pattern compared with the other three Malay populations. Besides, substantial differentiation was observed between the Malay populations from the north and the south, and between those from the west and the east. In summary, this study revealed that the genetic identity of the Malays comprises a mixed entity of multiple ancestries represented by Austronesian, Proto-Malay, East Asian and South Asian, with most of the admixture events estimated to have occurred 175 to 1,500 years ago, which in turn suggests that geographical isolation and independent admixture have significantly shaped the genetic architectures and the diversity of the Malay populations.

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