Dissecting the Genetic Affinity Between the Orang Asli and Southeast Asian Native Populations

ABSTRACT Introduction Southeast Asia (SEA) is a region with enriched human diversity and complex population history. Despite numerous small‐scale population genetics studies being carried out, the map of human migration in this landmass remains fragmentary. Notably, the genetic affinities of the Orang Asli from Peninsular Malaysia and other SEA natives have not been comprehensively assessed. Methods In this study, publicly available genotypic datasets were gathered and imputed. The genetic relationships and ancestry make‐up of 19 SEA native populations, covering Peninsular Malaysia, Indonesia, Papua New Guinea, the Philippines, Vietnam, and Andaman, were comprehended and benchmarked with 14 global populations. Results With ∼20 million SNPs coverage, we provided supporting evidence to (i) a possible ancient genetic link between the Andamanese, Papuan and the Philippines and Peninsular Negrito; (ii) gene flow from the ancestors of Andamanese to Papuan, and the Negrito from Peninsular Malaysia and the Philippines; (iii) different genetic structures between the island SEA (iSEA) and mainland (mSEA) populations; (iv) close genetic affinity between the Proto‐Malay Seletar with the iSEA populations and (v) close genetic affinity between the Senoi Mah Meri with the Proto‐Malays. Conclusion To our knowledge, this study reported the highest genomic sequence coverage and the most comprehensive SEA native populations covered thus far. Our results not only have provided strong supporting evidence to the earlier hypothesis, but also novel insights into the genetic diversity of the SEA native populations.