Population genetic structure of peninsular Malaysia Malay sub-ethnic groups

Abstract

Patterns of modern human population structure are helpful in understanding the history of human migration and admixture. We conducted a study on genetic structure of the Malay population in Malaysia, using 54,794 genome-wide single nucleotide polymorphism genotype data generated in four Malay sub-ethnic groups in peninsular Malaysia (Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis). To the best of our knowledge this is the first study conducted on these four Malay sub-ethnic groups and the analysis of genotype data of these four groups were compiled together with 11 other populations' genotype data from Indonesia, China, India, Africa and indigenous populations in Peninsular Malaysia obtained from the Pan-Asian SNP database. The phylogeny of populations showed that all of the four Malay sub-ethnic groups are separated into at least three different clusters. The Melayu Jawa, Melayu Bugis and Melayu Minang have a very close genetic relationship with Indonesian populations indicating a common ancestral history, while the Melayu Kelantan formed a distinct group on the tree indicating that they are genetically different from the other Malay sub-ethnic groups. We have detected genetic structuring among the Malay populations and this could possibly be accounted for by their different historical origins. Our results provide information of the genetic differentiation between these populations and a valuable insight into the origins of the Malay sub-ethnic groups in Peninsular Malaysia.

Figure 1. Neighbor-Joining tree of 15 populations based on Fst measurement.

In the square boxes are the four studied Malay sub-ethnic groups. Numbers at each branch are represent the percentage value of a thousand bootstrap replications and branches with bootstrap values less than 80% were condensed. The tree suggests a diverse origin of the Malay sub-ethnic groups that forms Cluster I, II and III. Notably, the position of MY-KN in Clade III is the most basal among other studied Malays supported by 100% of bootstrap replicates. There is a distinct genetic difference between the indigenous Orang Asli populations; the Negritos is oldest among the peopling groups in Malay Peninsula, whereas the Proto-Malays shared a common ancestry or have had some mixing with the Chinese and Javanese populations.

Figure 2. MDS analysis in three dimension model recapitulated the pattern of Fst tree.

The 3D MDS showed that all four Malay populations are well separated into three different sub-clusters, although still remained in the same cluster and dimensional platform. They are far separated from three other group populations which are Yoruba, Indian (IN-DR and IN-WL) and Negrito (MY-JH and MY-KS) which are far more diversified than the modern Malays.