POPULATION GENETIC DATASETS collected from various polymorphic genetic regions, either in the nuclear or mitochondrial genome, have contributed towards our understanding of ancient human origins and their migration patterns.

In Peninsular Malaysia, scientists have studied the DNA of different ethnic groups to learn more about their ancestral roots. These studies focus on genes that vary between people—like those related to blood types and immune responses—as well as parts of the genome that do not directly code for traits. By comparing these genetic patterns, researchers have found unique genetic markers in groups that are not closely related today. This suggests that Peninsular Malaysia was settled by multiple waves of people over thousands of years, which matches what archaeologists and linguists have also found (Figure 1).

The earliest inhabitants of Peninsular Malaysia are believed to be the Orang Asli (aborigines) of the Semang tribe, commonly known as Negritos. These nomadic hunter-gatherers, characterised by their short height, dark skin and curly hair, are said to be descendants of the first “anatomically modern humans” who migrated out of Africa 50,000 to 70,000 years ago. It is believed that they travelled overland via coastal routes to India, Indo-China and Peninsular Malaysia before spreading southeast to Papua New Guinea and Australia.

Today, although few Semang members have assimilated into mainstream society, others mainly live in small communities scattered across the mountainous forests of southern Thailand and northern Peninsular Malaysia, particularly in the states of Kedah, Perak and Kelantan (Figure 2). They communicate in Aslian languages, which is a branch of Austroasiatic languages—a trait they share with their larger Senoi brethren.

The semi-nomadic Senoi are believed to have migrated south from mainland Asia around 5,000 to 7,000 years ago. However, archaeological and linguistic data indicate that they did not settle further south on the peninsula, and their communities are mostly found in the central states of Perak, Selangor, Negeri Sembilan and Pahang.

Proto-Malays, on the other hand, are very distinct from the Semang and Senoi. They are mostly permanent coastal dwellers who speak Austronesian languages and practise an agricultural lifestyle. While they are primarily settled in the southern part of the peninsula, their kin may also be found in the wider regions of Southeast Asia and Oceania, with Taiwan as a potential distal source of their origin. Thanks to their seafaring and navigation skills, their descendants have spread out across the Indian and Pacific Oceans since 900 to 5,500 years ago. Studies have found genetic similarities between Malaysian Proto-Malays and natives from as far as Madagascar in Africa, to Aotearoa (indigenous name for New Zealand) and Rapa Nui (indigenous name for Easter Island) in Chile. On the Malay Peninsula, they are represented by the Orang Kanaq, Orang Kuala, Seletar, Jakun, Semelai and Temuan sub-tribes (Figure 2).

Throughout history, the Semang, Senoi and Proto-Malays interacted socially and culturally. This is supported by genetic data, where admixture has been detected in the genetic pools of all three aborigine tribes. As genetic materials are usually collected from modern samples, this admixture has complicated ancestral fraction determination, which is associated with genetic materials used for ancestral analysis. Further admixture on the peninsula occurred with the arrival of other distinct populations in relatively recent times, such as the Portuguese, Chinese and Indians during the height of the Melakan Empire in the 15th century. Peranakan communities resulted from cultural exchanges and intermarriages with local Malays.

Focus thus needs to be shifted to ancient specimens, which are less affected by admixture compared to modern human DNA. In this context, carbon-dated ancient human remains that are unearthed at various archaeological sites can be used to determine ancestral fraction in the gene pools of indigenous people, subsequently providing important data for ancestry studies. These include the Bewah Man excavated in 2010 in Gua Bewah, Terengganu, and the Penang Woman found in Guar Kepah in 2017. Ancient human remains have also been unearthed within caves in Perak (Gua Gunung Runtuh, Gua Teluk Kelawar, Gua Harimau, Gua Kajang and Gua Kerbau) and Kelantan (Gua Cha and Gua Peraling).

Several collaborative research projects are underway to generate the whole genome sequence of ancient DNA specimens in Malaysia, including the Bewah Man and Penang Woman. The institutions involved include Terengganu Museum, Sarawak Museum, Universiti Malaysia Terengganu, USM and the Malaysian Genome Research Consortium. International players include Griffith University in Australia, Copenhagen University in Denmark and the University of Auckland in New Zealand. These collaborations also focus on three other iconic ancient specimens: Deep Skull from Gua Niah, Sarawak (representing Borneo), and Yidinji King and Mungo Man discovered in Cairns and New South Wales, Australia, respectively. Together, combinations of ancient genomes analysed using cutting-edge methods can provide important reference sources for understanding the history of indigenous people in the Asia-Pacific region.

Working with ancient DNA samples is more challenging than analysing modern samples. The probability of obtaining good quality DNA depends on the nature of the specimens, as well as the type of bone available. Research has shown that high concentrations of DNA may be obtained from well-preserved petrous bones. However, in cases like the Bewah Man, the skull was simply not available and DNA extraction had to be performed on various bone fragments. In addition, ancient DNA work also requires a highly specialised laboratory to avoid contamination with modern samples.

Overall, improved understanding of early human settlements on the peninsula can potentially be achieved through population genetic datasets collected from contemporary descendants of indigenous populations for comparison with ancient specimens.

Through genetic research, scientists are slowly piecing together a more nuanced picture of prehistoric human mobility, interaction, adaptation and connection in this region. This offers a powerful approach towards reconstructing the demographic history of the peninsula.

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