The Origins Of Malaysian Indigenous Populations

A new study of the genetics of indigenous Malaysians finds that their ancestry is a mix of Hoabinhian hunter-gatherers, Neolithic farmers (probably from Southern China), and Austronesian speakers (a maritime population derived from an ancestral population from Taiwan with some Papuan admixture at some point), with some possible infusion also of people from the vicinity of India.

Southeast Asia comprises 11 countries that span mainland Asia across to numerous islands that stretch from the Andaman Sea to the South China Sea and Indian Ocean. This region harbors an impressive diversity of history, culture, religion and biology. 

Indigenous people of Malaysia display substantial phenotypic, linguistic, and anthropological diversity. Despite this remarkable diversity which has been documented for centuries, the genetic history and structure of indigenous Malaysians remain under-studied. To have a better understanding about the genetic history of these people, especially Malaysian Negritos, we sequenced whole genomes of 15 individuals belonging to five indigenous groups from Peninsular Malaysia and one from North Borneo to high coverage (30X). 

Our results demonstrate that indigenous populations of Malaysia are genetically close to East Asian populations. We show that present-day Malaysian Negritos can be modeled as an admixture of ancient Hoabinhian hunter-gatherers and Neolithic farmers. We observe gene flow from South Asian populations into the Malaysian indigenous groups, but not into Dusun of North Borneo. Our study proposes that Malaysian indigenous people originated from at least three distinct ancestral populations related to the Hoabinhian hunter-gatherers, Neolithic farmers and Austronesian speakers.

Farhang Aghakhanian, et al., "Sequence analyses of Malaysian Indigenous communities reveal historical admixture between Hoabinhian hunter-gatherers and Neolithic farmers" 12 Scientific Reports 13743 (August 12, 2022) (open access).

The introduction to the paper, as is often the case, provides some useful context:

Southeast Asia (SEA) has rich demographic, linguistic, and genetic diversity. The region is home to around 1249 ethnic groups belonging to five language families. Despite this fascinating diversity, the genetic history of the region remains under-studied and several outstanding gaps regarding the peopling of this region by anatomically modern humans (AMH) still exist. The four most-debated issues concerning the history of AMH in SEA relate to 1—The timing of their arrival in SEA; 2—Origins of hunter-gatherer populations in SEA and their relationship to the Hoabinhian culture; 3—Process of transition from foraging to farming lifestyle, and 4—Development of the cultural groups today recognized as Austroasiatic and Austronesian. According to archeological and early mitochondrial (mt) DNA investigations, the presence of AMH in SEA dates back to around 70–50 k years ago (kya). Later, genome-wide and ancient DNA studies postulated that the AMH entered the region following the “Out-of-Africa” human migration, perhaps via the southern coastal route, and subsequently spread into East Asia (EA), Papua New Guinea, and Australia. Subsequently, migrations from EA during the late-Pleistocene and Holocene, and population movements within the region, have shaped today’s population structure of SEA. The geographical location of Malaysia, a country that is physically split between mainland Asia and Borneo with significant population diversity, provides us with an opportunity to study the population history in SEA.

Malaysia is divided into a western part comprising Peninsular Malaysia and an eastern part on the Island of Borneo comprising the States of Sarawak and Sabah. Indigenous populations comprise 13.8% of the about 32 million population of Malaysia. The myriad indigenous communities of East and West express high ethno-linguistic and cultural diversity. The indigenous populations of Peninsular Malaysia are known as Orang Asli (“Original People” in the Malay language). They comprise 0.7% of the Peninsular Malaysia population and are divided into 3 major groups including Negrito, Senoi, and Proto-Malay based on their morphological and ethnolinguistic characteristics. 

Malaysian Negrito are hunter-gatherers who reside in the rain-forests of northern Peninsular Malaysia and are proposed to be descendants of the first settlers of Malaysia. They speak the Northern-Aslian dialect of the Austroasiatic (AA) language family, and their tradition involves egalitarianism and a patrilineal descent system. 

Senoi inhabit the central parts of Peninsular Malaysia. They speak the central and southern dialects of the Aslian language, and they traditionally practice slash-and-burn farming. 

Proto-Malay speak the Malay dialect of the Austronesian language family. They mainly live in the southern parts of Peninsular Malaysia. Proto-Malay practice farming and rain-forest harvesting and their traditions involve a marked social hierarchy. 

Each OA group is further subdivided into 6 subgroups, which makes up 18 OA subgroups. In Sarawak, the indigenous people are collectively known as Orang Ulu (“People of up-river land” in Malay) and comprise 40% of Sarawak’s population. The indigenous populations of Sabah make up 58.6% of Sabah’s population and are divided into 39 tribes. Dusun, Murut, Paitan, and Bajau are the major indigenous groups in Sabah.

Early anthropological studies proposed multiple competing theories about the origin of OAs. The “layer-cake” theory postulated that all three OA groups originated outside of Peninsular Malaysia and entered Malaysia at different times. Another theory by Benjamin (1985) proposed an in situ development and diversification of OAs following the first wave of human migration into Asia. 

Bellwood (1993) suggested that the ancestors of today Senois are associated with early Austroasiatic agriculturists who entered Peninsular during mid-Holocene era. Later interactions between these Neolithic farmers and local hunter-gatherers (ancestors of Negritos) resulted in language shift in Negritos as well as intermediate phenotypical features in Senois. He suggested that Proto-Malays originated from Austronesian speaking farmers who migrated to Malaysia during “Austronesian expansion” approximately 5–7 KYA. 

Early mtDNA studies found both haplogroups unique to Peninsular Malaysia, and those stablished in Indochina in OAs which suggest gene flow from neighboring populations in SEA into OAs. 

These studies identified two haplogroups of M21 and R21 in Negrito and Senoi with TMRCA around 30–50 KYA. Higher frequency of these two ancient haplogroups in Negritos could indicate that they are the most direct descendants of the earliest settlers of Peninsular Malaysia. 

Proto-Malay mainly harbor N21 and N22 haplogroups which may be associated with Austronesian expansion via Island Southeast Asia. 

Genotyping studies highlighted genetic affinity between Malaysian Negritos, Andamanese and Filipino Negritos. This may represent an ancient link between these populations. Whole genome-sequencing showed that Malaysian Negritos has the deepest divergence time from EA compared with the other two OA groups. This study also traced some level of gene flow from South Asia in OAs.

To advance our knowledge of the genetic structure and history of Malaysia’s indigenous people explore their relationship with the ancient hunter-gatherer and agriculturist communities of Malaysia, we performed high-coverage whole-genome analysis of 15 Orang Asli and Orang Ulu individuals including Negritos (Jehai, and Mendriq), Senoi (MahMeri), Proto-Malay (Seletar, and Jakun), and Dusun, and report the results of our analysis here.

The body text of the main analysis includes these highlights (with paragraph order and breaks rearranged for easier reading):

PCA and ADMIXTURE analysis. 

(A) ADMIXTURE analysis results at K = 5 of indigenous Malaysians, Andamanese, Malay, and selected HGDP-CEPH population samplesshowes that the ancestral component related to Southeast Asia (blue) is the most pronounced in OAs while ancestral components related to East Asia (yellow) and South Asia (green) are also present in most of OA groups. 

(B) Global PCA with indigenous Malaysian populations, Andamanese, Malay and selected HGDP-CEPH samples showes that OAs are in general genetically closer to East Asians while Malaysian Negritos have tendency towards Andaman islanders. 

(C) PCA representing ancient Southeast Asian with indigenous Malaysian, Andamanese, Malay and HGDP-CEPH populations from East Asia (EA), Central South Asia (CSA) and Oceania (OCE). Most of OAs positioned between Hoabinhian hunter-gatheres and ancient farmers. 

. . .

For mtDNA, we observed five haplogroups including R21, M21a, M13b1, M17a, and F1a1a in Malaysian Negritos. The TMRCAs of the R21, M21a, M17a, and F1a1a haplogroups have been dated to 8, 23, 19 and 8 kya, respectively, and have previously been reported In Malaysian and Thai hunter-gatherers. Haplogroup M13b has been dated to around 31 kya and observed in low frequency in Asia, specifically in Malaysia, Tibet, and Nepal.

MahMeri harbored the N22a haplogroup. Haplogroup N22a which was observed in MahMeri appears to be restricted to Peninsular Malaysia, although N22 has been recorded in low frequency elsewhere in SEA such as Philippine and Sumatra.

all Seletar carried N9a6b.  The N9a haplogroup is widespread in EA, SA, and SEA. However, its sub-clade N9a6 appears limited to mainland Southeast Asia (MSEA) and reaches the highest frequency in Peninsular Malaysia

Jakun carried the E1a2 haplogroup . . . We found two different haplogroups, M7c1c3 and R9c1a, in the Dusuns. The E1a, M711 [sic], R9c1 haplogroups are prevalent in island Southeast Asia (ISEA) and are widely believed to be associated with the Austronesian expansion.

For the Y chromosome, OA harbor the R1a1a1b2a, R2a, K2b, K2b1, and O2b1 haplogroups. 

The K2b haplogroup and its subclade K2b1, which were observed in Malaysian Negrito and Seletar, have been reported in other SEA Negritos and Oceania. 

Interestingly, we found haplotypes R2a and R1a1ab in Malaysian Negrito. Haplogroup R2a is mainly present in SA and at lower frequencies in Central, Southwest, and EA, while the R1a1a1b, and its sub-clades, comprise the major R1a sub-clades in Central and South Asia.

The concluding discussion notes that: 

Archeological and genetic evidence shows that the presence of AMH in Malaysia dates back to at least 40 kya. Between 13 to 3 kya Hoabinhian hunter-gatherers occupied the Peninsular. The Hoabinhian culture with a stone tool industry characterized by unifacial pebble tools, are believed to originate from south China and spread throughout mainland Southeast Asia (MSEA) and island Southeast Asia (ISEA). Since 4 kya, this South East Asian nation also witnessed at least two waves of migration from Neolithic farmers and Austronesian speakers.  . . .

While indigenous Malaysians are genetically closer to EA populations, consistent with previous studies, our new ADMIXTURE analysis revealed traces of South Asian ancestral component in OAs of Peninsular Malaysia. We could not detect this component in Dusun in Borneo. The presence of SA ancestral component in OAs has been previously reported. This ancestral component might be attributed to the first wave of human migration into SEA via the southern coastal route or later gene flow from SA during the expansion of Indian culture into Peninsular Malaysia in the first century A.D. Archeological sites in the state of Perak provide evidence of Hindu civilization. Being on the maritime route between China and South India, the Malay peninsula was involved in this trade. The Bujang Valley, being strategically located at the northwest entrance of the Strait of Malacca as well as facing the Bay of Bengal, was continuously frequented by Chinese and south Indian traders. Such was proven by the discovery of trade ceramics, sculptures, inscriptions and monuments dated from the 5th to fourteenth century CE. . . .

Analysis of OAs with ancient DNA from the Gua Cha revealed the contribution of populations genetically close to these samples into the Malaysian Negritos gene pool. The Gua Cha site is a rock shelter in northern Peninsular Malaysia. Based on Sieveking (1954), two archeological phases are recognizable at this site. The Hoabinhian phase when the shelter was used for habitation and occasionally for burial, and the Neolithic phase when it functioned as a cemetery. Radiocarbon dating showed that the Hoabinhian occupied the Gua Cha from 9 kya and later the Neolithic farmers used this site from 3 kya. Our outgroup-f3 analysis is consistent with the archeological findings regarding the transition from hunting-gathering to farming lifestyle in the Gua Cha cave. While the Ma911 (Hoabinhian layer) shared most alleles with the Malaysian Negritos, the Ma912 (Neolithic farmer) was closer to the Senoi agriculturists. Our results confirm that modern Malaysian Negritos have been derived genetically from two ancient populations: the Hoabinhian hunter-gatherers and the Neolithic farmers who originated from South China or MSEA.

Our analysis detected gene flow between different OA tribes, notably between Malaysian Negritos, with MahMeri and Jakun tribes. The admixture between neighboring OA tribes or between OAs and the Malay population has been reported previously. For example, Jinam et al. (2013) reported recent admixture between Jehai and their neighboring Malay, whereas such admixture was absent in Kensiu (another Negrito group). We did not find any traces of Negrito or Hoabinhian ancestry in Dusun. Likewise, Yew et al. (2018) reported the absence of Negrito ancestry in North Borneo, Dayak, and Bidayuh populations. Considering the demographical and archeological evidence which supports the presence of Austro-Melanesian people on Borneo Island, the best explanation for the absence of Negrito ancestry in Borneo could be the replacement of initial Austrolo-Melanesian inhabitants of the island by the Austronesians.

Interestingly, all the Seletar samples carried mtDNA N9a6b haplogroup. N96a haplogroup seems to be confined to the ISEA and reaches the highest frequency in Malaysia. Our results are consistent with Jinam et al. (2012) who reported only 4 mtDNA haplogroups (with N9a6b making up of 71% of mtDNA haplogroup frequency) in Seletar. Seletar are sea nomads who live along the strait of Johor (a waterway that separates Malaysia from Singapore). The history of Seletar is not well-documented. They are usually associated with the Orang Laut (“Sea people” in Malay), a conglomerate of sea nomad tribes who occupied the strait of Melaka. Our TreeMix and ROH results indicate that the Seletar are genetically closer to the Austronesian speakers, but they experienced severe genetic drift.