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Genetic structure and variation in Negrito, Senoi and Proto-Malay ethnic groups in Malaysia

posted on 23.02.2017, 23:25 by Aghakhanian Fereydani, Farhang
The indigenous populations of Peninsular Malaysia also known as “Orang Asli” or “original people” are putative isolated populations which comprise approximately 0.6 percent of Malaysia. Orang Aslis are categorized based on their demographic, linguistic and phonotypical characteristics in three subgroups namely Negrito, Senoi and Proto-Malay. The objective of this project was to study genetic structure in Orang Aslis through High-density SNP genotyping and Whole Genome Sequencing (WGS) technologies, and compare them to other population Southeast Asia. The results of our study showed that Malaysian Negritos are genetically distinct from other populations in East and Southeast Asia while other Orang Asli groups such as Senoi and Proto-Malay seemed to be admixed between Negritos and East Asians. We identified a genetic affinity between Andamanese and Malaysian Negritos which may suggest an ancient link between these two groups. Our results also showed gene flow between Austro-Asiatic speaking Orang Aslis and East Asian populations. The existence gene flow between these two major genetic components provided further evidences in support of an “Early Train” hypothesis, which suggests an early migration from Indochina or southern China to mainland Southeast Asia before the “Austronesian Expansion” and after “Out of Africa’ for human dispersal in Asia. Many novel genomic variants have also been discovered from whole-genome sequencing. We also found that Negrito, MahMeri, Seletar and Jakun communities are genetically isolated making them valuable resources for medical genetics researches. Our study also suggests that conventional categorization of Orang Aslis based on linguistics and anthropological characteristics may be incorrect.


Principal supervisor

Maude Elvira Phipps

Additional supervisor 1

Rakesh Naidu

Year of Award


Department, School or Centre

Jeffrey Cheah School of Medicine and Health Sciences (Monash University Malaysia)

Campus location



Doctor of Philosophy

Degree Type



Faculty of Medicine Nursing and Health Sciences