Abstract
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.
Highlights
In Malaysia, the Malays consist of several sub-groups, e.g., Melayu Minang, Melayu Jawa, Melayu Bugis and Melayu Kelantan, based on their respective geographical origins
Analyses were conducted by using 288,660 single nucleotide polymorphisms (SNPs) shared by 133 Malay individuals from Peninsular Malaysia, Singapore and Sri Lanka, as well as approximately 50,000 SNPs shared by 12 Indonesian Malays (IDM) located in Sumatra Island, 30 SGM and 38 PMM (20 Minangkabau, or locally known as Melayu Minang, a sub-tribe of Malay; 18 Kelantan Malay, or locally known as Melayu Kelantan) from the HUGO PanAsia SNP Consortium (PASNP)[8]
Based on the genetic distance measured by FST, SLM showed a closer relationship with South Asian populations (FST = 0.004–0.024) than with Southeast Asians (FST = 0 .010–0.057)
Summary
In Malaysia, the Malays consist of several sub-groups, e.g., Melayu Minang, Melayu Jawa, Melayu Bugis and Melayu Kelantan, based on their respective geographical origins. Malay sub-groups have various historical origins and genetic affinities[1,2] Both ancient and recent human activities have introduced gene flows from other populations into the Malays[3,4,5]. The Malays, especially those in the western and southern Malaysia, have had frequent interactions with other Austronesian populations through trading or other social activities[10] These early contacts did not result in a large-scale of population admixture, but intermarriage did exist. Some recent studies on Asian populations have included a few Malay samples from Malaysia, Indonesia and Singapore[8,14,15], but other Malay populations residing outside of Southeast Asia such as those living in Sri Lanka, have not been well studied. We inferred the population admixture history of each Malay population to illustrate the population genetic structure patterns
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