Unravelling the genetic history of Negritos and indigenous populations of Southeast Asia

• Main Authors: Farhang, Aghakhanian, Y, Yunus, R, Naidu, Timothy Adrian, Jinam, A, Manica, HB, Peng, Maude E., Phipps
• Format: Article
• Language: English
• Published: Oxford University Press 2015
• Subjects: QH426 Genetics
• Online Access: http://ir.unimas.my/id/eprint/42221/1/Unravelling%20the.pdf; http://ir.unimas.my/id/eprint/42221/; https://academic.oup.com/gbe/article/7/5/1206/604030?login=true

Indigenous populations of Malaysia known as Orang Asli (OA) show huge morphological, anthropological, and linguistic diversity. However, the genetic history of these populations remained obscure. We performed a high-density array genotyping using over 2 million single nucleotide polymorphisms in three major groups of Negrito, Senoi, and Proto-Malay. Structural analyses indicated that although all OA groups are genetically closest to East Asian (EA) populations, they are substantially distinct. We identified a genetic affinity between Andamanese and Malaysian Negritos which may suggest an ancient link between these two groups. We also showed that Senoi and Proto-Malay may be admixtures between Negrito and EA populations. Formal admixture tests provided evidence of gene flow between Austro-Asiatic-speaking OAs and populations from Southeast Asia (SEA) and South China which suggest a widespread presence of these people in SEA before Austronesian expansion. Elevated linkage disequilibrium (LD) and enrichedhomozygosityfoundinOAsreflectisolationandbottlenecksexperienced.EstimatesbasedonNe andLDindicatedthatthese populationsdivergedfromEastAsiansduringthelatePleistocene(14.5to8KYA).ThecontinuumindivergencetimefromNegritosto Senoi and Proto-Malay in combination with ancestral markers provides evidences of multiple waves of migration into SEA starting with the first Out-of-Africa dispersals followed by Early Train and subsequent Austronesian expansions.