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Dissecting the Genetic Affinity Between the Orang Asli and Southeast Asian Native Populations
Cengnata Alvin1, Tham Pei-Mei2, Foo Hoi-Thung2
1Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia.
Annals of Human Genetics
|June 30, 2025
Summary
This study reveals ancient genetic links and gene flow among Southeast Asian populations, including the Orang Asli. It highlights distinct genetic structures between island and mainland Southeast Asia (SEA) groups.
Area of Science:
- Population Genetics
- Human Migration Studies
- Genomic Diversity Analysis
Background:
- Southeast Asia (SEA) exhibits rich human diversity and complex population history.
- Previous genetic studies in SEA have been small-scale, leaving migration patterns fragmented.
- The genetic relationships of Orang Asli and other SEA natives require comprehensive assessment.
Purpose of the Study:
- To comprehensively assess the genetic affinities of Orang Asli and other Southeast Asian native populations.
- To reconstruct migration patterns and understand genetic diversity across SEA.
- To benchmark SEA populations against global genetic diversity.
Main Methods:
- Gathered and imputed publicly available genotypic datasets.
- Analyzed genetic relationships and ancestry of 19 SEA native populations.
- Compared 19 SEA populations with 14 global populations using ~20 million SNPs.
Main Results:
- Provided evidence for ancient genetic links between Andamanese, Papuan, Philippines, and Peninsular Negrito groups.
- Identified gene flow from Andamanese ancestors to Papuan and Negrito populations.
- Showcased distinct genetic structures between island SEA (iSEA) and mainland SEA (mSEA) populations.
- Revealed close genetic affinity of Proto-Malay Seletar with iSEA populations.
- Demonstrated close genetic affinity of Senoi Mah Meri with Proto-Malays.
Conclusions:
- This study offers the highest genomic sequence coverage and most comprehensive population data for SEA natives to date.
- Results strongly support existing hypotheses on SEA population genetics and migration.
- Novel insights into the genetic diversity and historical connections of Southeast Asian native populations were uncovered.
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