Ancient Genomic Insights into Prehistoric Populations of the Malay Peninsula and Their Connections to Present-Day Indigenous Communities

Ahmad Faiz Shazwan Bin Abdul Malik1*, Odongoo Ravdandorj2, Zuliskandar Bin Ramli3, Dato’ Dr. Mohd Zaki Salleh4, Lay Kek Teh5, and Takashi Gakuhari6

The historical, religious, cultural, and linguistic diversity of Southeast Asia has been shaped by multiple waves of human migration. Various theories, supported by archaeological, linguistic, anthropological, and genetic evidence, have been proposed to explain these migrations. The Malay Peninsula played a crucial role in prehistoric human movements. However, ancient DNA studies remain limited, despite the discovery of over 50 burials in the Nenggiri Valley, which are linked to pre-Neolithic (Hoabinhian) and Neolithic farming populations. The main challenge in genetic analysis is the poor preservation of collagen and endogenous DNA. The site’s location, situated between the territories of the Semang (traditionally hunter-gatherers) and the Senoi (traditionally farmers), provides key evidence for prehistoric human admixture. We have successfully obtained new genomic sequences from human remains at the Gua Cha site. Principal Component Analysis (PCA), outgroup-f3 statistics, f4 statistics, and qpAdm results indicate high genetic affinity between these individuals, previously sequenced neighbouring ancient populations, and modern Indigenous groups in Malaysia as well as other modern Southeast Asian populations. Admixture tests were conducted to identify potential migration groups that contributed to the cultural development of these sites and to examine gene flow among ancient and modern populations, including the Indigenous groups. This research enhances our understanding of human migration and admixture in the region. The findings provide new genetic insights into ancient population dynamics and their connections to modern Southeast Asian populations.