Genetic relatedness of indigenous ethnic groups in northern Borneo to neighboring populations from Southeast Asia, as inferred from genome-wide SNP data

Chee Wei Yew, Mohd Zahirul Hoque, Jacqueline Pugh-Kitingan, Alexander Minsong, Christopher Lok Yung Voo, Julian Ransangan, Sophia Tiek Ying Lau, Xu Wang, Woei Yuh Saw, Rick Twee Hee Ong, Yik Ying Teo, Shuhua Xu, Boon Peng Hoh, Maude E. Phipps, S. Vijay Kumar

Research output: Contribution to journalArticleResearchpeer-review

7 Citations (Scopus)


The region of northern Borneo is home to the current state of Sabah, Malaysia. It is located closest to the southern Philippine islands and may have served as a viaduct for ancient human migration onto or off of Borneo Island. In this study, five indigenous ethnic groups from Sabah were subjected to genome-wide SNP genotyping. These individuals represent the “North Borneo”-speaking group of the great Austronesian family. They have traditionally resided in the inland region of Sabah. The dataset was merged with public datasets, and the genetic relatedness of these groups to neighboring populations from the islands of Southeast Asia, mainland Southeast Asia and southern China was inferred. Genetic structure analysis revealed that these groups formed a genetic cluster that was independent of the clusters of neighboring populations. Additionally, these groups exhibited near-absolute proportions of a genetic component that is also common among Austronesians from Taiwan and the Philippines. They showed no genetic admixture with Austro-Melanesian populations. Furthermore, phylogenetic analysis showed that they are closely related to non–Austro-Melansian Filipinos as well as to Taiwan natives but are distantly related to populations from mainland Southeast Asia. Relatively lower heterozygosity and higher pairwise genetic differentiation index (FST) values than those of nearby populations indicate that these groups might have experienced genetic drift in the past, resulting in their differentiation from other Austronesians. Subsequent formal testing suggested that these populations have received no gene flow from neighboring populations. Taken together, these results imply that the indigenous ethnic groups of northern Borneo shared a common ancestor with Taiwan natives and non–Austro-Melanesian Filipinos and then isolated themselves on the inland of Sabah. This isolation presumably led to no admixture with other populations, and these individuals therefore underwent strong genetic differentiation. This report contributes to addressing the paucity of genetic data on representatives from this strategic region of ancient human migration event(s).

Original languageEnglish
Pages (from-to)216-226
Number of pages11
JournalAnnals of Human Genetics
Issue number4
Publication statusPublished - Jul 2018


  • Genetic structure
  • genome-wide SNPs
  • indigenous ethnic groups
  • northern Borneo

Cite this