Beyond Religion
A Genetic Perspective on Indigenous Identity in the Indonesian Archipelago

The debate over who can be categorized as indigenous versus settler in the Indonesian archipelago has long persisted in Indonesian political and social discourse. Often, these categorizations have been based on cultural factors such as religion and beliefs. However, this approach ignores more fundamental biological and genealogical aspects. This article explores an alternative perspective that views concepts of indigenous and settler populations as connected to ancestral lineage and genetic identity, rather than merely religious identities that can change over time.
Indigenous and Settler Populations: A Genetic and Genealogical Perspective
In the fields of biological anthropology and population genetics, indigenous identity is associated with human groups that have inhabited a geographical area since prehistoric times, long before the formation of modern states. Dr. Stephen Oppenheimer, a genetics expert from Oxford University, explains in his book "Eden in the East" (1998) that determining indigenous status should be based on chronology of arrival and genetic traces that can be tracked through DNA, not on changeable cultural identities such as religion or language.
"We can trace human migration paths through genetic markers that are inherited from generation to generation. This is an identity that cannot be changed, unlike religion or language which can be adopted or abandoned," writes Oppenheimer (1998).
Professor Peter Bellwood from the Australian National University, a leading archaeologist who studies migration patterns in Southeast Asia, strengthens this argument in his work "Prehistory of the Indo-Malaysian Archipelago" (2007). Bellwood states: "In the context of the Indonesian archipelago, the determinant of indigenous status is the presence of ancestors in the region since prehistoric times, which can be reconstructed through archaeological and genetic evidence" (Bellwood, 2007).
Dr. Herawati Sudoyo, a genetics researcher from the Eijkman Institute for Molecular Biology (now part of BRIN), through her research on mitochondrial DNA of Indonesian populations, found that the genetic identity of the archipelago's inhabitants was formed long before the influence of major religions. "Our DNA stores a record of ancestral migrations that cannot be manipulated. This is a fundamental identity that cannot be changed like religious identity," she explained in an interview (Sudoyo, 2015).
Migration History and Settlement of the Indonesian Archipelago
The Indonesian archipelago has been inhabited by various waves of human migration for tens of thousands of years. Based on genetic and archaeological evidence, several major waves of settlement can be identified:
Early Inhabitants (70,000-50,000 Years Ago)
The first wave of settlement occurred approximately 70,000-50,000 years ago when anatomically modern humans (Homo sapiens) began to spread from Africa. According to research published in Nature by Dr. Murray Cox and team (2016), this first group entered the Sundaland region (land now mostly submerged beneath the Java Sea and Strait of Malacca) via the South Asian route.
Genetic analysis shows that populations such as the Mentawai in Sumatra, and some groups in the interior of Borneo and Papua have genetic markers that can be traced back to this early migration wave. This makes them indigenous populations in the most fundamental sense (Cox et al., 2016).
Austronesian Migration (4,500-3,000 Years Ago)
Around 4,500-3,000 years ago, a major migration wave occurred from Taiwan southward, bringing rice farming technology, Proto-Austronesian language, and megalithic culture. Research by Dr. J. Stephen Lansing from the University of Singapore shows that this Austronesian migration spread to almost the entire archipelago and formed the genetic basis of most modern Indonesians (Lansing et al., 2011).
Professor Truman Simanjuntak from the National Archaeological Research Center argues: "Austronesian migration brought revolutionary changes in the lifestyle of the archipelago's inhabitants, from foragers to farmers. However, this did not mean eliminating previous populations, but rather genetic mixing occurred" (Simanjuntak, 2017).
Indian Influence (Early CE - 15th Century)
From the early Common Era until the 15th century, intensive contact with Indian civilization brought Hindu-Buddhist influences to the archipelago. Dr. Daud Ali, a historian from the University of Pennsylvania, asserts that this was more a process of cultural transmission than mass population migration. "What happened was the adoption of Indian cultural and religious elements by local elites, not a mass movement of people from India" (Ali, 2011).
DNA analysis conducted by an international research team led by Dr. Mark Stoneking from the Max Planck Institute shows that the genetic influence from India on Indonesian populations is relatively small compared to its massive cultural transmission (Stoneking et al., 2013).
Chinese Influence (Since Early CE)
Contact with China has existed since the early Common Era, but significant migration only occurred in later periods, especially during the Ming and Qing dynasties. Professor Leonard Blussé from Leiden University in his work "Strange Company: Chinese Settlers, Mestizo Women and the Dutch in VOC Batavia" (1986) explains that Chinese migration to the archipelago occurred in several distinct waves.
"Modern genetic analysis shows that although there is a Chinese diaspora in various port cities of the archipelago, its genetic influence is limited to certain regions and does not change the genetic composition of the majority of the islands' inhabitants," writes Dr. Yan Junxin from the Chinese Academy of Sciences in his research on Southeast Asian population genetics (Yan, 2018).
Islamization (13th to 18th Centuries)
The process of Islam entering the archipelago took place from the 13th to 18th centuries through maritime trade networks. Professor Azyumardi Azra, a historian from UIN Syarif Hidayatullah Jakarta, in his book "Networks of Middle Eastern Scholars and the Indonesian Archipelago in the 17th and 18th Centuries" (2004) emphasizes that the Islamization of the archipelago was more cultural and intellectual than demographic.
"Islamization in the archipelago was a complex process involving adaptation and negotiation between local culture and Islamic teachings, not population replacement," writes Azra (2004). This is reinforced by genetic research by Dr. Tatiana Karafet from the University of Arizona who found that the spread of Islam in Indonesia was not accompanied by significant changes in population genetic structure (Karafet et al., 2010).
Implications for Modern Citizenship Concepts
Dr. Benedict Anderson, in his classic work "Imagined Communities" (1983), explains that the concept of modern nationality should transcend primordial ties such as ethnicity or religion. However, understanding genealogical roots remains important for appreciating the diversity that shapes national identity.
Professor Robert Cribb from the Australian National University argues that in the context of modern Indonesia, "Recognition of the diversity of genetic origins and historical migrations actually strengthens the narrative of the nation as a cultural mosaic that has been interacting for thousands of years" (Cribb, 2010).
Conclusion
From a genetic and genealogical perspective, the concepts of indigenous and settler populations are more appropriately linked to chronology of arrival and traceable genetic footprints, rather than changeable cultural identities such as religion or beliefs. Genetic and archaeological evidence shows that the Indonesian archipelago has been a meeting point for various waves of human migration for tens of thousands of years.
Understanding the genetic history and migration patterns in the archipelago can provide a more objective foundation for discussing issues of identity and citizenship. This approach allows for appreciation of the genetic and cultural diversity that has shaped Indonesia, while avoiding the politicization of identity that is often based on non-fundamental factors such as adopted religions or beliefs.
As stated by Dr. Dienekes Pontikos, a population genetics researcher: "Our DNA carries the story of ancestral journeys that are much older and more fundamental than the cultural identities we adopt" (Pontikos, 2019). Thus, discussions about who is indigenous and who is a settler should be based on scientific evidence about the chronology and continuity of presence in a region, not on cultural factors that can change over time.
References :
Ali, D. (2011). The Early Inscriptions of Indonesia and the Problem of the Sanskrit Cosmopolis. Oxford University Press.
Anderson, B. (1983). Imagined Communities: Reflections on the Origin and Spread of Nationalism. Verso.
Azra, A. (2004). Jaringan Ulama Timur Tengah dan Kepulauan Nusantara Abad XVII dan XVIII. Kencana.
Bellwood, P. (2007). Prehistory of the Indo-Malaysian Archipelago. Australian National University Press.
Blussé, L. (1986). Strange Company: Chinese Settlers, Mestizo Women and the Dutch in VOC Batavia. Foris Publications.
Cox, M., et al. (2016). "Genetic History of Indigenous Populations of Indonesia." Nature, 538, 201-205.
Cribb, R. (2010). Digital Atlas of Indonesian History. NIAS Press.
Karafet, T., et al. (2010). "Major East-West Division Underlies Y Chromosome Stratification across Indonesia." Molecular Biology and Evolution, 27(8), 1833-1844.
Lansing, J. S., et al. (2011). "An Ongoing Austronesian Expansion in Island Southeast Asia." Journal of Anthropological Archaeology, 30(3), 262-272.
Oppenheimer, S. (1998). Eden in the East: The Drowned Continent of Southeast Asia. Weidenfeld & Nicolson.
Pontikos, D. (2019). Genetic Origins and Modern Identity. Cambridge Scholars Publishing.
Simanjuntak, T. (2017). Austronesian Diaspora: A New Perspective. Gadjah Mada University Press.
Stoneking, M., et al. (2013). "Genomic Insights into the Population Structure of the People of India." Proceedings of the National Academy of Sciences, 110(15), 6022-6027.
Sudoyo, H. (2015). "Genetic Diversity and History of Indonesian Populations." Interview at the National Seminar on Indonesian Population Genetics, Jakarta.
Yan, J. (2018). "Genetic Structure of Southeast Asian Populations and the Regional Pattern of Chinese Influence." Journal of Human Genetics, 63(3), 455-466.
About the Creator
Defrida
Writing is how I create my own universe of thought. Without it, I'd vanish into the swirling depths of a black hole.




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