Population Genetic Structure of Peninsular Malaysia Malay Sub-Ethnic Groups

Wan Isa Hatin,Ab Rajab Nur-Shafawati,Mohammed Rizman-Idid,Li Jin,Shuhua Xu,Bin Alwi Zilfalil,Mohd-Khairi Zahri,Soon-Guan Tan,Henry Harpending

doi:10.1371/journal.pone.0018312

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.

Highlights

Malays (Melayu) are an ethnic group who speak MalayoPolynesian language which is a member of the Austronesian family [1,2]
The single nucleotide polymorphisms (SNPs) genotype data of 71 unrelated individual of four Malay sub-ethnic groups namely Melayu Kelantan, Melayu Minang, Melayu Jawa and Melayu Bugis were generated by Affymetrix GeneChip Mapping Xba 50 K Array, a microarray chip that enabled researchers to screen over 50,000 SNPs loci in each individual
The tree does not support the designation of Malays as a monophyletic group since the Melayu Kelantan (MY-KN) were on a separated clade from other Malay populations, and the MY-JV were more closely related to Proto-Malays and Chinese than other

Summary

Introduction

Malays (Melayu) are an ethnic group who speak MalayoPolynesian language which is a member of the Austronesian family [1,2]. They predominantly inhabit the Malay Peninsula, the east coast of Sumatra and the coast of Borneo [1]. In Peninsular Malaysia, the Malays consist of various sub-ethnic groups which are believed to have different ancestral origins based on their migrations centuries ago [3]. The Malay populations in the western (Melayu Minang) and southern parts (Melayu Jawa and Melayu Bugis) of the Peninsular Malaysia were believed to have had more historical and cultural links with the populations from the Indonesian archipelago compared to the

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