Five Stages Colonization Model

Indonesia is one of the most varied regions on earth in terms of ethnic, linguistic and genetic diversity. Past changes in global climate have had an especially strong influence in this island nation. Lands in the west, now largely submerged homeland, Sundaland. In the east, Pleistocene’s Sahul linked New Guinea and Australia into a single continent. And in between the two, Wallacea-wonderland, where islands-hopping required by our ancestors to cross from Sunda to Sahul. Following the end of the Last Glacial Maximum, ice melting in the Arctic fueled a rapid rise in global sea levels.

The human history of Indonesia played out against the backdrop of this dynamically changing geography. Settled by anatomically modern humans at least 60,000 years ago, and perhaps much earlier, evidence of early hunter-gatherer groups throughout the Pleistocene found. The biggest cultural change occurred within the last 10,000 years when the archaeological record abruptly chronicles the appearance of agricultural communities together with pottery, plant cultivation and animal domestication.

Indonesian genetic diversity has largely been shaped by two forces: population movements driven by sea level changes, and by farming populations expanding from the Asian mainland into the islands Southeast Asia.

Population Diversity

The Indonesian archipelago consists of over 17,000 islands of various sizes. In general, the western side of the archipelago has much larger islands than the eastern side. For example, the Moluccas island group consists of 1,000 smaller islands scattered across the eastern side of the archipelago (Bellwood 1985, Taylor 2003). The geography of some islands, particularly the presence of mountain ranges, forms obstacles to communication between different local populations and could represent barriers to gene flow. For example, Sulawesi has four peninsulas and each has a mountain range that joins in the centre of the island (Mattulada 1978). Although approximately 6,000 of the islands in the Indonesian archipelago are inhabited, the majority of the 240 million inhabitants are dispersed across a small number of larger islands (i.e. Sumatra, Java, Kalimantan, Sulawesi, Nusa Tenggara and Papua).

Indonesia is home to over 300 traditional groups, each with their own language or dialect, religious belief and culture (Bellwood 1985). The majority (80%) of Indonesia’s population adheres to Islam. The other 20% of the population belong to various religions, including Christianity (Roman Catholic and Protestant), Buddhist and Hindu religions (practiced only in Bali) and other indigenous, local religions. This diversity is a result of the evolutionary history of the archipelago. Towns and cities in Indonesia are mainly inhabited by people who identify with the traditional group of the area. However, many locations in Java have inhabitants from various non-Javanese traditional groups who have relocated for work or education.

The diversity of the Indonesian population is particularly evident in the linguistic profile of the country. Indonesia is home to 726 languages, of which 719 are living. The living languages of Indonesia represent 10.45% of all living languages worldwide (Lewis 2009). The majority of Indonesian languages are classified into the Austronesian family, while others are Papuan in origin, a strong indication of the evolutionary history of the region (Tryon 1985, Lewis 2009).

Genetic population sub-structure in Indonesia

Over time a number of genetically distinct subpopulations have developed throughout Indonesia as the result of a number of population migrations and the presence of barriers to gene flow within the archipelago. Furthermore, given that geography and language are two significant barriers to gene flow, it was expected that these genetic subpopulations would reflect predetermined geographical and linguistic population boundaries.

Y-chromosome reflects the history of Indonesian men, emphasizing a complex multifaceted history of the region’s islands and communities. A partial history of Indonesia’s women, piecing together 60,000 years of population movements that have shaped the diversity of Indonesians living today. By comparison with Y-chromosome, we can contrast the histories of Indonesian men and women, presenting common patterns of shared inheritance with key points of demographic and social difference.

In the west of the archipelago, all individuals from the inner Mentawai subpopulation have close to 100% inferred ancestry from a single population, which could suggest that this ancestral population arose through genetic drift acting on an isolated group of Austronesian language speakers. Individuals from coastal Mentawai and Nias also have high proportions (approximately 50%) of ancestry to the single ancestral population. Virtually all mtDNA haplogroups detected in Nias have an Asian origin and no strong indications of population sub-structure were observed. In contrast, the initial pre-screening of a sample subset indicated that 100% of individuals possessed the O-M175 NRY haplogroup. When 14 additional Y-SNPs that specifically characterise O-M175 and its sub lineages were genotyped, only two NRY haplogroups were detected in 407 individuals from Nias (O-M119*, 70% and O-M110, 30%). Both O-M119* and O-M110 are believed to have an Asian origin. The haplogroup distributions indicate population sub-structure within the island, with O-M110 being restricted to South Nias, where it is found at high frequency (van Oven et al. 2011a). The high frequency of O-M110 in Nias (and its absence from most neighbouring populations) is most likely the result of a genetic bottleneck/founder event followed by subsequent isolation and genetic drift within the Nias population. Linguistic evidence supports this finding of population isolation, with the languages of the Barrier Islands (of which Mentawai and Nias are part of) occupying a deep rooted branch within the Austronesian language phylogeny without close neighbours (Gray et al. 2009).

At the other side of the archipelago, individuals from the Papuan subpopulation (for example, Sentani) also have high proportions of ancestry from a Melanesian population. Individuals from Flores and Sumba also have high proportions of ancestry from the Melanesian population. The third ancestral population Asian/Austronesian is most prevalent (approaching 100%) in the subpopulations from Java and Bali. Populations from Sumatra and Sulawesi also have significant ancestry from this Asian/Austronesian population.

Research conducted by Karafet et al. (2010) on the Y chromosomes of 1,917 individuals from 32 geographic subpopulations within Indonesia represents the most thorough ancestry informative analysis performed in the region thus far. Haplogroup frequencies in West Indonesian and East Indonesian populations are strikingly different. In West Indonesia, O-P203, O-M95* and O-M119* collectively account for 60% of the Y chromosomes but much lower frequencies of these haplogroups are found in East Indonesia (<10%). These haplogroups are of Asian origin. Meanwhile, Melanesian haplogroups C-M38*, M-P34 and S-M254 collectively account for more than 50% of East Indonesian Y chromosomes and are absent from West Indonesia. While sparse sampling from Sulawesi and other Central Indonesian islands meant that Karafet et al. (2010) could not determine the exact location of the population boundary between West and East Indonesia. Sea levels were much lower (-120 m below current level), most modern islands had merged into larger landmasses and the westernmost parts of Indonesia were physically contiguous with mainland Asia.

Indonesian population history

The first stage involved the arrival of individuals carrying Y DNA haplogroups D, C and F, and mtDNA M, N and R approximately 65,000 years ago, from which East Indonesian and Melanesian populations have inherited high proportions of C-M38, M-P256 and S-M230 Y chromosomes. This first stage recorded by deep mtDNA lineages.

  • N21 branches directly from the N founder node and was earlier thought to have originated in ISEA (Sundaland, region of Sumatra) and subsequently spread to West Malaysia based on control region sequence. N21 lineages in Temuan appeared to be derived from an ancestral type found in the Cham of Vietnam, implying an origin in Indochina during Pleistocene (29,300 +/- 15,500 years ago) and it’s dispersal appears to be limited to Sundaland which encompassed West Malaysia, Sumatra even up to the Alor islands.
  • N22 appears to be limited to the Temuan, although it appears very low frequencies in the Philippines, Sumatra and Sumba islands. Like N21, the coalescent time of 24,800 +/- 13,800 years ago suggests deep ancestry in Sundaland
  • R21 appears to be limited to Negrito populations in West Malaysia (Jahai Semang), although it was also found at appreciable frequencies in the Senoi, suggesting gene flow between the indigenous Negrito with the incoming Senoi from Indochina. All R21 lineages coalesce with haplogroup P4, found mostly in Australian Aborigines and Papuans, at approximately 47,000 +/- 5100 years ago possibly linking the Negritos with the first migration to the SE Asian region (southern coastal routes) populations where it is found at low frequencies in Sumatra and Java, Indonesia, but not in the Philippines or Taiwan.
  • R22 found in mainland Southeast Asia and the Nicobar Islands is also found across southern ISEA. Most of these rare lineages appear to date to the Pleistocene. Coalescence time in SE Asia was calculated to be 28,300 years ago. Haplogroup R22 now appears to be most common in the Shompen group of the Nicobar Islands; however, it is most diverse in ISEA, and the root type is only found in Lombok and Alor, suggesting that it could be an indigenous marker for that area.
  • R23, small clade found in Bali and Sumba, coalescence time

Which trace back to the main branching of macrohaplogroups M and N, and have a spotty distribution across both mainland and island southeast Asia today.

The second stage of Indonesian colonization bought several major clades of haplogroup K-M526* (M-P34, S-M230, NO-M214) approximately 50,000 years ago.

The third stage involved mtDNA haplogroup M9 and its subclades (E) around 36,000 years ago through the Last Glacial Maximum, and subsequently the dispersals of K subclades out of Sundaland, and the dispersals of mtDNA haplogroup B and its subclades (better known as Polynesian motif, B4a1a1a1) in the last ice age.

Stage four involved major Y DNA haplogroup O (O-M119, O-M95, O-P203 and O-M122) from the Asian mainland post glacial maximum. The Austronesian expansion approximately 4,200 years ago represents the fourth stage of Indonesian colonization. This stage correlates with the expansion of Austronesian languages throughout the region and Karafet et al. (2010) proposed that haplogroups O-P201 and possibly O-M110 and O-P203 entered both West and East Indonesia during this stage.

Finally, Karafet et al. (2010) detected a handful of minor genetic signatures that appear to be correlated with three historical migrations into Indonesia that have had lasting social and cultural influences. Fifth stage, haplogroups linked to the introduction of Hinduism (haplogroups H, R and Q) and the spread of Islam (haplogroups J, L and R) are found throughout western Indonesia but particularly in Java and Bali, while the Chinese haplogroup O-M7 is also present at considerable levels in Java (11%) and Borneo (20%).

Indonesia’s closest genetic connections lie toward mainland and island Southeast Asia rather than Oceania. Western Indonesia groups largely owing to low levels of mtDNA haplogroups P and Q. The Polynesian motif spread westward from Spice Islands (Halmahera, homeland of ancestors of Lapita people), and similar movements have been proposed to explain the distribution of Papuan languages in eastern Indonesia.

Analysis of Austronesian languages and cultural systems, as well as autosomal markers, suggests that the men and women of ISEA have followed quite different social histories. Genetic divisions between populations are far weaker for mtDNA than for Y-chromosome STRs, and this effect is even more pronounced at the haplogroup level when Indonesia is separated into its eastern and western parts (post-glaciation). This discrepancy suggests that men and women have had different patterns of dispersal, with women moving widely between communities, while men have historically stayed local. Patrilocality, men remain in their natal community, but women move to the home village of their husband. Interestingly, matrilineal systems are thought to have dominated ancestral Austronesian societies. Patrilocality could instead be the long-term standard with a transient switch to matrilocality during the Austronesian era (in eastern Indonesia).

15 responses to “About

  1. I’ve never imagined that there is an Indonesian guy writing and compiling such a comprehensive information on population genetics/human evoution in a blog. Saya baru saja berencana mau memulai, eh ternyata sudah ada.. mantab !
    boleh tau alamat emailnya mas/mba? barangkali bisa diskusi lebih lanjut, mumpung bidang penelitiannya sama..

    • Terima kasih Mas Pradiptajati, Anda lebih berkompeten di bidang populasi genetik (temuan Y-DNA C7 dan C9 di populasi orang laut itu cukup sensasional, semoga dikembangkan terus untuk C yang lain (M38), khususnya di Wallacea dan Sahul).
      Saya hanya popgen enthusiast, yang tertarik dengan sejarah populasi negeri ini. Boleh saling email di mozardien@gmail.com Saya juga ingin belajar lebih banyak lagi.

      • Apakah Admin bersedia untuk menuliskan hasil observasi sementara, terkait dengan konten blog ini, ke http://bersains.wordpress.com ? Kami ada kajian khusus untuk sains dan matematika populer, yang didistribusikan dalam bentuk ebook resmi. Jika tidak keberatan, kami sangat senang untuk berbagi perspektif. Terima kasih

      • Saya tidak keberatan untuk kepentingan penyebaran informasi, hanya saja, untuk sejarah populasi Indonesia terkendala oleh data yang masih parsial, dan bukti-bukti baru terus muncul seiring waktu. Seperti yang terbaru dari Sulawesi, yang bisa dikategorikan dalam pra-gelombang pertama, bisa mengubah skenario pendudukan Sunda dan Wallacea. Saya sedang menyusun untuk gelombang ketiga dan keempat, dengan godaan pra-gelombang pertama yang terus muncul, saya tidak tahu kapan akan selesai.

        Apakah hanya garis besar saja yang dibutuhkan, atau detail skenario dari masing-masing gelombang pendudukan Nusantara?

      • Diskusi menarik terutama berkenaan dengan analisis DNA dari Harvard Medical School, semoga konteksnya penelitian Reich et al. tentang Denisovan dan pendudukan Asia Tenggara. Saya support Sundaland theory, karena bukti genetika sangat mendukung. Konteks Sundaland theory yang saya support pada rentang waktu Jaman Es berakhir, dan awal era Holocene, terkait dengan sebaran populasi penutur proto-Malayo-Polynesia Untuk kaitan dengan Gunung Padang sangat sirkumstansial, cenderung kurang. Jika bisa menempatkan artefak dari Gunung Padang pada rentang waktu yang saya sebutkan (13-8kya), mungkin relasi yang dicari akan mendapat jawaban.

        Saya coba selesaikan naskah secepatnya.

      • Naskah yang ringkasan TFM 2015 itu sudah bisa menjadi pembuka perspektif tentang Sundaland Theory dari sudut sebaran genetik, karena Bersains adalah untuk umum, sains populer. Apakah Admin blog sedang di Indonesia? Jika di Jakarta, apakah berkenan berbagi perspektif keilmuan terkait Sundaland ini ke publik, dalam forum diskusi terbuka, non formal? Terima kasih sebelumnya.

      • Saya di Bandung, namun rasanya kurang pas untuk bicara di forum yang isinya bisa jadi mahasiwa dan kalangan akademik, karena saya tidak ada background akademik soal genetika, paleoantropologi maupun arkeologi. Saya hanya mengikuti data-data penelitian yang ada, mencoba menarik kesimpulan dari berbagai disiplin ilmu yang sering ‘disembunyikan’ oleh peneliti karena afiliasi dengan institusi penyandang dana atau karena mempertahankan prestige masa lalu. Saya memperhatikan ada ketidakberesan/bias antara dua kubu besar yang ‘bersaing’ [Out of Africa dan Multiregional, beserta yang tidak setuju keduanya]. Karena itu saya mencoba merekonstruksi ulang, mencari benang merah antara kedua kubu yang ‘berseteru’.

        Silakan pakai materi yang ada, saya sudah posting di blog dan website, artinya publik boleh menggunakan untuk keperluan penyebaran informasi dan pengetahuan.

        Dari gelombang pertama dan kedua sebenarnya sudah kelihatan bahwa populasi di Sunda-Sahul itu tidak ada kaitan dengan out of Africa. Common ancestor dari populasi Nusantara kemungkinan besar mengalami diferensiasi di sekitar Sichuan, China Selatan. Baru dapat genetik marker dari China Selatan, root dari manusia modern juga ada di sana [L3, yang menurunkan N, M, dst]. Sedangkan root manusia modern di Afrika seperti mandeg [L0, L1, L3 yang tidak menurunkan N, M, dst dengan alasan migrasi] tidak mengalami diferensiasi selama ~120 ribu tahun. Tidak masuk akal.

        Sedangkan out of Sundaland yang sebenarnya untuk meng-counter out of Taiwan berkenaan dengan penutur Austronesia/Malayo Polynesia. Data genetika dan artefak bisa membuktikan bahwa proto-Malayo-Polynesia adalah mereka yang tinggal di wilayah antara timur laut Borneo dan barat laut Sulawesi ketika Jaman Es berakhir. Yang ini belum sempat di blog.

        Sedangkan leluhur Polynesian motif adalah populasi dari Wallacea. Sudah ada semua di blog.

  2. Pak, Salam kenal! Saya sangat salut dengan tulisan Bapak yang sangat jelas dan terperinci! Keep going, Pak!

    • Salam kenal Chelzie, senang sekali yang ingin tahu leluhur bangsa Indonesia makin bertambah.
      Update selalu disisipkan di bagian bawah masing-masing artikel, tidak dibuat laman tersendiri. Jadi, jangan kelewat 🙂


  3. ”Stage four involved major Y DNA haplogroup O (O-M119, O-M95, O-P203 and O-M122) from the Asian mainland post glacial maximum. The Austronesian expansion approximately 4,200 years ago represents the fourth stage of Indonesian colonization. This stage correlates with the expansion of Austronesian languages throughout the region and Karafet et al. (2010) proposed that haplogroups O-P201 and possibly O-M110 and O-P203 entered both West and East Indonesia during this stage.”

    O-M95 is Austro-Asiatic marker, which you didn’t mention at all. I think O-M95 came earlier than O-M119. Autosomal DNA also show similarity of (at least) modern population of Java with modern Khmer and Thai population. We knew that many modern Thai are Mon-Khmer stock that had been assimilated into Tai Kradai speaker.

    So it’s possible that some population in Indonesia (especially in Java and Borneo) used to be Austro-Asiatic speaker before switch to be Austronesian speaker after the arrival of O-M119.

    • That’s one possibility. New study offers another possibility, that both mainland Asian and Austronesian ancestries were introduced across Indonesia during a single event. Also, if you take a look at Loyang Mendale archaeological site di Gayo, Aceh, there is evidence of continuity between Hoabinhian and Austronesian culture between 5-4 kya. They lived together for few thousand years in the same cave.
      Other possibility is O2a1-M95 who migrated southward (from Vietnam) were already Austronesian speakers as listed in figure 3 here.
      And you wouldn’t expect that O-M122 in Indonesia (O3-N6 lineage) is completely different lineage from Southern China O-M122 (O3-M324), which often times to be associated with those that speak a Sinitic, Tibeto-Burman, or Hmong–Mien language, yet they spread all across the archipelago. One should re-genotyping all O-M122 samples with B451 mutations to prove Indonesian samples are different lineage than its distant cousins in the north.
      This five stages colonizations is based on Karafet et al. five years back. I kinda lazy to update this page, because everything is uncertain, until we have some solid evidence from aDNA in ISEA. Pain Haka burials in Flores is sequenced by Max Planck right now, so we’ll see.
      I’ll update this page when we have some solid multidisciplinary evidences.

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