Haplogroup D and Migration out of Africa: Andamanese, Negrito, and Orang Asli Peoples

Damien Marie AtHope’s Art

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“Scarification involves scratching, etching, burning/branding, or superficially cutting designs, pictures, or words into the skin as a permanent body modification or body art. The body modification can take roughly 6–12 months to heal. In the process of body scarification, scars are purposely formed by cutting or branding the skin by various methods (sometimes using further sequential aggravating wound-healing methods at timed intervals, like irritation). Scarification has been traditionally practiced by darker skinned cultures, possibly because it is usually more visible on darker skinned people than tattoos. It was common in indigenous cultures of Africa (especially in the west), Melanesia, and Australia. Some indigenous cultures in North America also practiced scarification, including the ancient Maya.” ref

A Rare Deep-Rooting D0 African Y-Chromosomal Haplogroup and Its Implications for the Expansion of Modern Humans Out of Africa

“Present-day humans outside Africa descend mainly from a single expansion out ∼50,000–70,000 years ago, but many details of this expansion remain unclear, including the history of the male-specific Y chromosome at this time. Here, we reinvestigate a rare deep-rooting African Y-chromosomal lineage by sequencing the whole genomes of three Nigerian men described in 2003 as carrying haplogroup DE* Y chromosomes, and analyzing them in the context of a calibrated worldwide Y-chromosomal phylogeny. We confirm that these three chromosomes do represent a deep-rooting DE lineage, branching close to the DE bifurcation, but place them on the D branch as an outgroup to all other known D chromosomes, and designate the new lineage D0. We consider three models for the expansion of Y lineages out of Africa ∼50,000–100,000 years ago, incorporating migration back to Africa where necessary to explain present-day Y-lineage distributions. Considering both the Y-chromosomal phylogenetic structure incorporating the D0 lineage, and published evidence for modern humans outside Africa, the most favored model involves an origin of the DE lineage within Africa with D0 and E remaining there, and migration out of the three lineages (C, D, and FT) that now form the vast majority of non-African Y chromosomes. The exit took place 50,300–81,000 years ago (latest date for FT lineage expansion outside Africa – earliest date for the D/D0 lineage split inside Africa), and most likely 50,300–59,400 years ago (considering Neanderthal admixture). This work resolves a long-running debate about Y-chromosomal out-of-Africa/back-to-Africa migrations, and provides insights into the out-of-Africa expansion more generally.” ref

“Haplogroup D, also known as D-CTS3946, is a Y-chromosome haplogroup. Like its relative distant sibling, haplogroup E-M96, D-CTS3946 has the YAP+ unique-event polymorphism, which defines their parent, haplogroup DE. D-CTS3946 has two basal branches, D1 and D2. D1 and D2 are found primarily in East Asia, at low frequency in Central Asia and Southeast Asia, and at very low frequency in Western Africa and Western Asia. Haplogroup D was formerly the name of the D lineage D-M174. Varying proposals exist regarding the origin of haplogroup DE, the parent of D, with some suggesting an African and a few others an Asian origin.” ref

“Haber et al. (2019) identified a haplogroup, termed “D0”, in three Nigerians. Defined by the SNP A5580.2, “D0” haplogroup is outside M174, but belongs to the D lineage, shares 7 SNPs with it D-M174 that E lacks, and was determined to have diverged early from the D branch (near the D/E split). Haber et al. (2019) considered several possibilities, including an African origin and Asian origin for the haplogroup, but in part because of the deep-rooting of haplogroup “D0”, as well as recently calculated early divergence times for it and its parent haplogroup, DE, the authors conclude in favor of an African origin for D0 and DE, as well as for the common ancestor (now known as D-CTS3946 or “D”) of D0 and D-M174.” ref

“According to Haber et al. (2019), D0 is a branch of the DE lineage near the D/E split but on the D branch, diverging around 71,000 years ago. The authors find divergence times for DE*, E, and D0, all likely within a period of about 76,000-71,000 years ago, and a likely date for the exit of the ancestors of modern Eurasians out of Africa (and ensuing Neanderthal admixture) later, at around 50,300-59,400 years ago, which they argue, also supports an African origin for those haplogroups. Thus, D-CTS3946 is proposed to have spread both within and outside of Africa, with one branch diverging into D0 in Africa and another branch that left Africa eventually diverging into D-M174 (i.e., with the M174 mutation later arising from the D-CTS3946 that had spread to Asia).” ref

“Hallast et al. (2020), on ancient and modern haplogroups using a phylogenetic analysis of haplogroup C, D and FT sequences, including very rare deep-rooting lineages (such as D0/D2 sampled by Haber et al. 2019) argues, taking the “rare deep-rooted D0” into account, that the initial splits within haplogroup CT (ancestor of DE) occurred in Africa. They also argue that phylogeographic analyses of ancient and present-day non-African Y chromosomes, all point to East/Southeast Asia as the origin 55,000–50,000 years ago of all known surviving non-African male lineages (apart from recent migrants) soon after an initial 70–55,000 year ago migration from Africa of basal haplogroup D and other basal y-lineages.” ref

“They argue that these lineages then rapidly expanded across Eurasia, later diversified in southeast Asia and then expanded westwards around 55,000–50,000 years ago, replacing other local lineages within Eurasia, and conclude that haplogroup D (as D-M174) then underwent rapid expansions within Eastern-Eurasian populations and consists of 5 different branches which formed about 45,000 years ago. They find that these haplogroups currently have their greatest diversity in Eastern Eurasia (east/southeast Asia). Tibeto-Burmese populations of East and Southeast Asia were found to have the highest amount of diversity.” ref

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Haplogroup D

“D1 and D2 are found primarily in East Asia, at low frequency in Central Asia and Southeast Asia, and at very low frequency in Western Africa and Western Asia.” ref

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Ongan peoples

“The Onge (also Önge, Ongee, and Öñge) are an Andamanese ethnic group, indigenous to the Andaman Islands in Southeast Asia at the Bay of Bengal, India. They are traditionally hunter-gatherers and fishers, but also practice plant cultivation. They are designated as a Scheduled Tribe of India. The native Andamanese religion and belief system is a form of animism. Ancestor worship is an important element in the religious traditions of the Andaman islands. The Andamanese probably had no government or clan leader, but made decisions by group consensus. The Onge speak the Önge language. It is one of two known Ongan languages (southern Andamanese languages). Önge used to be spoken throughout Little Andaman as well as in smaller islands to the north, and possibly in the southern tip of South Andaman island.” ref

“Genetically, the Onge, as well as other Andamanese people, are distantly related to East Asian people. The Andamanese Onge show the highest affinity towards some Southeast Asian Negrito ethnic groups, such as the Aeta people, but also ancient remains of Hoabinhians, which are all characterized by Basal-East Asian ancestry. It was found that Andamanese (Onge) split from the common ancestor of modern day East Asians between 50,000 to 25,000 BCE, before becoming isolated on the Andaman Islands. The Andamanese (Onge) as well as East Asians, are also distantly related to the Indigenous population of South Asia. Recent genetic evidence suggest that a Basal-East Asian population (close or ancestral to Andamanese and East Asians) was widespread in Asia and contributed to the formation of modern South Asians (Indian people).” ref

“A study by Reich et al. (2009) found that while the Onge are distantly related to modern Indian people, they have none of the admixture from Neolithic Iranian farmers or steppe pastoralists which is widespread on the mainland. From this, they conclude that the Onge are solely descended from one of the ancient populations which contributed to the genetics of modern Indians. According to Chaubey and Endicott (2013), overall, the Andamanese are more closely related to Southeast Asians and East Asians than they are to present-day South Asians. According to Yelmen et al. 2019, certain South Indian tribal groups are a better proxy for Ancient Ancestral South Asian (AASI) ancestry than the Andamanese Onge are.” ref

“The Onge population is consistently declining and infant mortality rate is very high. Several physiological parameters such as ABO, Rh blood group, blood pressure, SGOT, SGPT and total protein level, Hepatitis B surface antigen, VDRL and some genetic markers have been conducted. The results of blood pressure, cholesterol level and liver enzyme test do not show any abnormality. However, the incidence of HbsAg is found to be very high that might have affected their fertility. Analysis of paternal lineages indicates that all Onge carry the Y-DNA Haplogroup D, widespread in East Asia and less in Central Asia. Maternally, the Onge also exclusively belong to the M clade, bearing the M2 and M4 subclades, commonly found in Asia.” ref

“Proposed migration routes of East Asian paternal lineages, including haplogroup D branches and its branches. Andamanese displays a high frequency of D1a2b (previously known as D1a3).” ref

“When compared with ancient DNA samples, Andamanese peoples are closest to the pre-Neolithic Hoabinhians in Mainland Southeast Asia (covered by two samples from Malaysia and Laos), and display high genetic affinity to the Tianyuan man in Northern China, with both being basal to contemporary East Asians, forming a “deep Asian” ancestral lineage. Deep Asian ancestry (Tianyuan/Onge) contributed to the Peopling of Southeast Asia.” ref

Andaman Islands

“The Andaman Islands (/ˈændəmən/) are an archipelago, made up of 200 islands, in the northeastern Indian Ocean about 130 km (81 mi) southwest off the coasts of Myanmar‘s Ayeyarwady Region. Together with the Nicobar Islands to their south, the Andamans serve as a maritime boundary between the Bay of Bengal to the west and the Andaman Sea to the east. Most of the islands are part of the Andaman and Nicobar Islands, a Union Territory of India, while the Coco Islands and Preparis Island are part of the Yangon Region of Myanmar.” ref

“The Andaman Islands are home to the Andamanese, a group of indigenous people made up of a number of tribes, including the Jarawa and Sentinelese. While some of the islands can be visited with permits, entry to others, including North Sentinel Island, is banned by law. The Sentinelese are generally hostile to visitors and have had little contact with any other people. The Indian government and coast guard protect their right to privacy. The climate is typical of tropical islands of similar latitude. It is always warm, but with sea breezes. Rainfall is irregular, usually dry during the north-east monsoons, and very wet during the south-west monsoons.” ref

“The oldest archaeological evidence for the habitation of the islands dates to the 1st millennium BCE. Genetic evidence suggests that the indigenous Andamanese peoples share a common origin, and that the islands were settled sometime after 26,000 years ago, possibly at the end of the Last Glacial Period, when sea levels were much lower reducing the distance between the Andaman Islands and the Asian mainland, with genetic estimates suggesting that the two main linguistic groups diverged around 16,000 years ago. Andamanese peoples are a genetically distinct group highly divergent from other Asians.” ref

Andamanese People

“The Great Andamanese are an indigenous people of the Great Andaman archipelago in the Andaman Islands. Historically, the Great Andamanese lived throughout the archipelago, and were divided into ten major tribes. Their distinct but closely related languages comprised the Great Andamanese languages, one of the two identified Andamanese language families. The Great Andamanese were clearly related to the other Andamanese peoples, but were well separated from them by culture, language, and geography. The languages of those other four groups were only distantly related to those of the Great Andamanese and mutually unintelligible; they are classified in a separate family, the Ongan languages.” ref

“They were once the most numerous of the five major groups in the Andaman Islands, with an estimated population between 2,000 and 6,600, before they were killed or died out due to diseases, alcohol, colonial warfare, and loss of hunting territory. Only 52 remained as of February 2010; by August 2020, there were 59. The tribal and linguistic distinctions have largely disappeared, so they may now be considered a single Great Andamanese ethnic group with mixed Burmese, Hindi, and aboriginal descent. The Great Andamanese are classified by anthropologists as one of the Negrito peoples, which also include the other four aboriginal groups of the Andaman islands (Onge, Jarawa, Jangil, and Sentinelese) and five other isolated populations of Southeast Asia. The Andaman Negritos are thought to be the first inhabitants of the islands, having emigrated from the mainland tens of thousands of years ago.” ref

“The Andamanese are the various indigenous peoples of the Andaman Islands, part of India‘s Andaman and Nicobar Islands, the union territory in the southeastern part of the Bay of Bengal. The Andamanese are a designated Scheduled Tribe in India’s constitution. The Andamanese peoples are among the various groups considered Negrito, owing to their dark skin and diminutive stature. All Andamanese traditionally lived a hunter-gatherer lifestyle, and appear to have lived in substantial isolation for thousands of years. It is suggested that the Andamanese settled in the Andaman Islands around the latest glacial maximum, around 26,000 years ago.” ref

“The Andamanese peoples included the Great Andamanese and Jarawas of the Great Andaman archipelago, the Jangil of Rutland Island, the Onge of Little Andaman, and the Sentinelese of North Sentinel Island. Among the Andamanese, a division of two groups can be made. One is more open to contact with civilization, and the other is hostile and resistant to communicating with the outer world. At the end of the 18th century, when they first came into sustained contact with outsiders, an estimated 7,000 Andamanese remained. In the next century, they experienced a massive population decline due to epidemics of outside diseases and loss of territory. Today, only roughly over 500 Andamanese remain, with the Jangil being extinct. Only the Jarawa and the Sentinelese maintain a steadfast independence, refusing most attempts at contact by outsiders.” ref

“The oldest archaeological evidence for the habitation of the islands dates to the 1st millennium BCE. Genetic evidence suggests that the indigenous Andamanese peoples share a common origin, and that the islands were settled sometime after 26,000 years ago, possibly at the end of the Last Glacial Period, when sea levels were much lower reducing the distance between the Andaman Islands and the Asian mainland, with genetic estimates suggesting that the two main linguistic groups (Great Andamanese and Onge/Jarawa) diverged around 16,000 years ago. It was previously assumed that the Andaman ancestors were part of the initial Great Coastal Migration (South-Eurasians or Australasians) that was the first expansion of humanity out of Africa, via the Arabian peninsula, along the coastal regions of the South Asia towards Insular Southeast Asia, and Oceania.” ref

“The Andamanese were considered to be a pristine example of a hypothesized Negrito population, which showed similar physical characteristics, and was supposed to have existed throughout southeast Asia. The existence of a specific Negrito-population is nowadays doubted. Their commonalities could be the result of evolutionary convergence and/or a shared history. Recent genetic studies conclusively demonstrate Negrito groups do not share a common origin to the exclusion of other Asians. The four major groups of Andamanese. By the end of the eighteenth century, there were an estimated 5,000 Great Andamanese living on Great Andaman. Altogether they comprised ten distinct tribes with different languages. The population quickly dwindled to 600 in 1901 and to 19 by 1961. It has increased slowly after that, following their move to a reservation on Strait Island. As of 2010, the population was 52, representing a mix of the former tribes.” ref

“The Jarawa originally inhabited southeastern Jarawa Island and have migrated to the west coast of Great Andaman in the wake of the Great Andamanese. The Onge once lived throughout Little Andaman and now are confined to two reservations on the island. The Jangil, who originally inhabited Rutland Island, were extinct by 1931: the last individual was sighted in 1907. Only the Sentinelese are still living in their original homeland on North Sentinel Island, largely undisturbed, and have fiercely resisted all attempts at contact. The Andamanese languages are considered to be the fifth language family of India, following the Indo-European, Dravidian, Austroasiatic, and Sino-Tibetan. While some connections have been tentatively proposed with other language families, such as Austronesian, or the controversial Indo-Pacific family, the consensus view is currently that Andamanese languages form a separate language family – or rather, two unrelated linguistic families: Greater Andamanese and Ongan.” ref

Until contact, the Andamanese were strict hunter-gatherers. They did not practice cultivation, and lived off hunting indigenous pigs, fishing, and gathering. Their only weapons were the bow, adzes, and wooden harpoons. The Andamanese knew of no method for making fire in the nineteenth century. They instead carefully preserved embers in hollowed-out trees from fires caused by lightning strikes. The men wore girdles made of hibiscus fiber which carried useful tools and weapons for when they went hunting. The women on the other hand wore a tribal dress containing leaves that were held by a belt. A majority of them had painted bodies as well. They usually slept on leaves or mats and had either permanent or temporary habitation among the tribes. All habitations were man made.” ref

“Some of the tribe members were credited with having supernatural powers. They were called oko-pai-ad, which meant dreamer. They were thought to have an influence on the members of the tribe and would bring misfortune to those who did not believe in their abilities. Traditional knowledge practitioners were the ones who helped with healthcare. The medicine that was used to cure illnesses were herbal most of the time. Various types of medicinal plants were used by the islanders. 77 total traditional knowledge practitioners were identified and 132 medicinal plants were used. The members of the tribes found various ways to use leaves in their everyday lives including clothing, medicine, and to sleep on.” ref

“Anthropologist A.R. Radcliffe Brown argued that the Andamanese had no government and made decisions by group consensus. The native Andamanese religion and belief system is a form of animism. Ancestor worship is an important element in the religious traditions of the Andaman islands. Andamanese Mythology held that humans emerged from split bamboo, whereas the women were fashioned from clay. One version found by Alfred Reginald Radcliffe-Brown held that the first man died and went to heaven, a pleasurable world, but this blissful period ended due to breaking a food taboo, specifically eating the forbidden vegetables in the Puluga‘s garden. Thus Catastrophe ensued, and eventually the people grew overpopulated and didn’t follow Puluga‘s laws, and hence there was a Great Flood that left four survivors, who lost their fire.” ref

“Negritos, specifically Andamanese, are grouped together by phenotype and anthropological features. Three physical features that distinguish the Andaman islanders include: skin color, hair, and stature. Those of the Andaman islands have dark skin, are short in stature, and have “frizzy” hair, while displaying “Asiatic facial features”.Dental characteristics also group the Andamanese between Negrito and East-Asian samples. When comparing dental morphology the focus is on overall size and tooth shape. To measure the size and shape, Penrose’s size and shape statistic is used. To calculate tooth size, the sum of the tooth area is taken. Factor analysis is applied to tooth size to achieve tooth shape. Results have shown that the dental morphology of Andaman Islanders resembles that of tribal populations of South Asia (Adivasi) the most, followed by Philippine Negrito groups, contemporary Southeast Asians, and East Asians. The tooth size of the Andamanese was found to be most similar to that of Han Chinese and Japanese.” ref

“Genetic analysis, both of nuclear DNA and mitochondrial DNA provide information about the origins of the Andamanese. Genetic studies agree that Great Andamanese as well as Onge and Jawara, share a common origin to the exclusion of other Asians, and that they are highly genetically divergent from other Asian populations. The Andamanese show a very small genetic variation, which is indicative of populations that have experienced a population bottleneck and then developed in isolation for a long period.” ref

“An allele has been discovered among the Jarawas that is found nowhere else in the world. Blood samples of 116 Jarawas were collected and tested for Duffy blood group and malarial parasite infectivity. Results showed a total absence of both Fya and Fyb antigens in two areas (Kadamtala and R.K Nallah) and low prevalence of both Fya antigen in another two areas (Jirkatang and Tirur). There was an absence of malarial parasite Plasmodium vivax infection though Plasmodium falciparum infection was present in 27·59% of cases. A very high frequency of Fy (a–b–) in the Jarawa tribe from all the four jungle areas of Andaman Islands along with total absence of P. vivax infections suggests the selective advantage offered to Fy (a–b–) individuals against P. vivax infection.” ref

“Genetic studies have revealed that the Andamanese people display affinity to the indigenous South Asian hunter-gatherers, often termed “Ancient Ancestral South Indians” (AASI), as well as to Australasian populations (AA), such as Melanesians, and contemporary East/Southeast Asian peoples (ESEA). While the Andamanese are occasionally used as an imperfect proxy for the AASI component, they are genetically closer to the ‘Basal East Asian’ Tianyuan man.” ref

“Phylogenetic data suggests that an early initial eastern lineage trifurcated, and gave rise to Australasians (Oceanians), the AASI, Andamanese, as well as East/Southeast Asians, although Papuans may have also received some geneflow from an earlier group (xOoA), around 2%, next to additional archaic admixture in the Sahul region. Concerning the use of Andamanese as proxy for AASI ancestry, Yelmen et al. (2019) deduced that the non West Eurasian component, termed S-component, extracted from South Asian samples would serve as a much better proxy for AASI ancestry, especially those extracted from Irula samples, than the Andamanese. Overall, the Malaysian Negritos (Semang), such as the Maniq people, Jahai people, and Batek people, are the closest modern living relatives of the Andamanese people.” ref

When compared with ancient DNA samples, Andamanese peoples are closest to the pre-Neolithic Hoabinhians in Mainland Southeast Asia (covered by two samples from Malaysia and Laos), and display high genetic affinity to the Tianyuan man in Northern China, with both being basal to contemporary East Asians, forming a “deep Asian” ancestral lineage. Deep Asian ancestry (Tianyuan/Onge) contributed to the Peopling of Southeast Asia. The male Y-chromosome in humans is inherited exclusively through paternal descent. All sampled males of Onges (23/23) and Jarawas (4/4) belong to a sublineage of D-M174(D1a3). However, male Great Andamanese do not appear to carry these clades. A low resolution study suggests that they belong to haplogroups K, L, O, and P1 (P-M45).” ref

“A 2017 study by Mondal et al. finds that the Y-chromosome of the Riang people (a Tibeto-Burmese population), sublineage D1a3 (D-M174*) and the Andamanese D1a3 (*D-Y34637) have their nearest related lineages in East Asia, splitting about 23,000 years ago from an East Asian-related population. The Jarawa and Onge shared this D1a3 lineage with each other within the last ~7,000 years, suggesting a bottleneck event. They further suggest that: “This strongly suggests that haplogroup D does not indicate a separate ancestry for Andamanese populations. Rather, haplogroup D was part of the standing variation carried by the OOA expansion, and later lost from most of the populations except in Andaman and partially in Japan and Tibet”. Other haplogroups found among Andamanese include haplogroup P, and L-M20.” ref

“Several studies (Hammer et al. 2006, Shinoda 2008, Matsumoto 2009, Cabrera et al. 2018) suggest that the paternal haplogroup D-M174 originated somewhere in Central Asia. According to Hammer et al., haplogroup D-M174 originated between Tibet and the Altai mountains. He suggests that there were multiple waves into Eastern Eurasia. In a 2019 study by Haber et al. showed that Haplogroup D-M174 originated in Central Asia and evolved as it migrated to different directions of the continent. One group of population migrated to Siberia, others to Japan and Tibet, and another group migrated to the Andaman islands.” ref

“Bulbeck (2013) shows the Andamanese maternal mtDNA is entirely mitochondrial Haplogroup M. Haplogroup M (mtDNA) is a descendant of haplogroup L3, typically found in Eurasia and parts of Africa. The mtDNA M is found in all Onge and most of the Great Andamanese samples. Analysis of mtDNA, which is inherited exclusively by maternal descent, confirms the above results. Haplogroup M is, however, also the single most common mtDNA haplogroup in Asia, where it represents 60% of all maternal lineages. Haplogroup M is also relatively common in Northeast Africa of Somalis, Oromo at over 20%. Also in the Tuareg in Mali and Burkina Faso at 18.42%.” ref

“Unlike some Negrito populations of Southeast Asia, Andaman Islanders have not been found to have Denisovan ancestry. However, they are estimated, like all other non-African populations, to possess approximately 1-2% Neanderthal ancestry. A 2019 study concluded that all Asian and Australo-Papuan populations, including Andaman Islanders, also share between 2.6 and 3.4% of the genetic profile of a previously unknown hominin that was genetically roughly equidistant to Denisovans and Neanderthals.” ref

Negrito

“The term Negrito (/nɪˈɡriːtoʊ/; lit. ’little black people‘) refers to several diverse ethnic groups who inhabit isolated parts of Southeast Asia and the Andaman Islands. Populations often described as Negrito include: the Andamanese peoples (including the Great Andamanese, the Onge, the Jarawa, and the Sentinelese) of the Andaman Islands, the Semang peoples (among them, the Batek people) of Peninsular Malaysia, the Maniq people of Southern Thailand, as well as the Aeta of Luzon, the Ati and Tumandok of Panay, the Mamanwa of Mindanao, and about 30 other officially recognized ethnic groups in the Philippines.” ref

“Based on perceived physical similarities, Negritos were once considered a single population of closely related people. However, genetic studies suggest that they consist of several separate groups descended from the same ancient East Eurasian meta-population that gave rise to modern East Asian peoples and Oceanian peoples, as well as displaying genetic heterogeneity. The Negritos form the indigenous population of Southeast Asia, but were largely absorbed by Austroasiatic- and Austronesian-speaking groups who migrated from southern East Asia into Mainland and Insular Southeast Asia with the Neolithic expansion. The remainders form minority groups in geographically isolated regions.” ref

“Genetic studies provided mixed evidence of modern Negrito populations, with admixtures in different. Studies indicate that Negrito populations are closer to their neighboring non-Negrito communities in their paternal heritage and overall DNA on average. It has been found that the physical and morphological phenotypes of Negritos, such as short stature, a wide and snub nose, curly hair and dark skin, “are shaped by novel mechanisms for adaptation to tropical rainforests” through convergent evolution and positive selection, rather than a remnant of a shared common ancestor, as suggested previously by some researchers.” ref

“A Negrito-like population was most likely also present in Taiwan before the Neolithic expansion and must have persisted into historical times, as suggested by evidence from morphological features of human skeletal remains dating from around 6,000 years ago resembling Negritos (especially Aetas in northern Luzon), and further corroborated by Chinese reports from the Qing period rule of Taiwan (1684 to 1895) and from tales of Taiwanese indigenous peoples about people with “dark skin, short-and-small body stature, frizzy hair, and occupation in forested mountains or remote caves.” ref

“The word Negrito, the Spanish diminutive of negro, is used to mean “little black person.” This usage was coined by 16th-century Spanish missionaries operating in the Philippines, and was borrowed by other European travellers and colonialists across Austronesia to label various peoples perceived as sharing relatively small physical stature and dark skin. Contemporary usage of an alternative Spanish epithet, Negrillos, also tended to bundle these peoples with the pygmy peoples of Central Africa on the basis of perceived similarities in stature and complexion. (Historically, the label Negrito has also been used to refer to African pygmies.) The appropriateness of bundling peoples of different ethnicities by similarities in stature and complexion has been called into question.” ref

“There are over 100,000 Negritos in the Philippines. In 2010, there were 50,236 Aeta people in the Philippines. The Ati people 55,473 (2020 census) Officially, Malaysia had approximately 4,800 Negrito (Semangs). This number increases if we include some of the populations or individual groups among Orang Asli who have either assimilated Negrito population or have admixed origins. According to the 2006 census, the number of Orang Asli was 141,230  Andamanese of India with just c. over 500. Thailand Negrito Maniq is estimated 300, divided into several clans. Other puts it at 382 or less than 500. Most groups designated as “Negrito” lived as hunter-gatherers, while some also used agriculture, such as plant harvesting. Today most live assimilated to the majority population of their respective homeland. Discrimination and poverty are often problems, caused either by their lower social position and/or their hunter-gatherer lifestyles.” ref

The Y-chromosome landscape of the Philippines: extensive heterogeneity and varying genetic affinities of Negrito and non-Negrito groups

“Abstract: The Philippines exhibits a rich diversity of people, languages, and culture, including so-called ‘Negrito’ groups that have for long fascinated anthropologists, yet little is known about their genetic diversity. We report here, a survey of Y-chromosome variation in 390 individuals from 16 Filipino ethnolinguistic groups, including six Negrito groups, from across the archipelago. We find extreme diversity in the Y-chromosome lineages of Filipino groups with heterogeneity seen in both Negrito and non-Negrito groups, which does not support a simple dichotomy of Filipino groups as Negrito vs non-Negrito. Filipino non-recombining region of the human Y chromosome lineages reflect a chronology that extends from after the initial colonization of the Asia-Pacific region, to the time frame of the Austronesian expansion. Filipino groups appear to have diverse genetic affinities with different populations in the Asia-Pacific region. In particular, some Negrito groups are associated with indigenous Australians, with a potential time for the association ranging from the initial colonization of the region to more recent (after colonization) times. Overall, our results indicate extensive heterogeneity contributing to a complex genetic history for Filipino groups, with varying roles for migrations from outside the Philippines, genetic drift, and admixture among neighboring groups.” ref

“The Philippines figures prominently in two significant demographic events in the Asia-Pacific region. The first was the initial colonization of Sunda and Sahul around 40–50 thousand years ago to which the human fossil remains from Tabon Cave, Palawan in the Philippines, with estimated ages ranging from 14,000 to 58,000 years ago, may be associated. The second was the Austronesian expansion, which is proposed to have originated in Taiwan around 5,000–6,000 years ago, and spread first to the Philippines before continuing to Southeast Asia, Near and Remote Oceania, and Madagascar.4 The impact of the Austronesian expansion is evidenced by the fact that all Philippine languages today are Austronesian.5 In addition, a popularly accepted ‘waves of migration theory’ suggests that the origins and diversity of people in the Philippines was the result of several migrations into the archipelago during the periods of low water levels, when there existed land bridges with the Sunda shelf via Palawan and the Sulu Archipelago, and with Celebes via Mindanao.” ref

“Currently, over 170 Filipino ethnolinguistic (FE) groups are recognized on the basis of language and culture. Of these FE groups, anthropologists have traditionally been most interested in those with short stature, frizzy hair, and dark skin color, historically defined as ‘Negrito’ groups. There are more than 20 FE Negrito (FEN) groups in the Philippines. It has been proposed that Negrito groups represent a separate migration out of Africa. Although all FEN groups currently speak Austronesian languages, it has been proposed that they originally spoke non-Austronesian languages, which were subsequently replaced by Austronesian languages. This view, along with their physical features and hunter-gatherer mode of subsistence, has resulted in the historical depiction of the FEN groups as the aboriginal, first occupants of the archipelago, and as such, the popular distinction of FEN vs non-Negrito FE (FEnN) groups has been perpetuated.” ref

“To date, no comprehensive genetic diversity study of FE groups has been presented. A mitochondrial DNA (mtDNA) study on Philippine populations showed further support for the ‘out of Taiwan’ hypothesis for the Austronesian expansion, as well as identifying rare mtDNA haplotypes; however, samples were not from specific FE groups, but from urban populations, and from Filipinos living in Taiwan. Early studies have inferred genetic differences between some FEN groups (the Aeta of Bataan, Aeta of Zambales and the Mamanwa) and possible affinities with populations, such as indigenous Australians and Papuan groups. A recent genome-wide study on Asian populations included six FEN groups, but only one other FEnN group, and three urban populations.” ref

“We, therefore, report a survey of genetic variation in the non-recombining region of the human Y chromosome (NRY) of 16 FE groups (six FEN and 10 FEnN groups). Our results indicate that, a simple division of FEN vs FEnN groups is not supported by the NRY evidence. Instead, FE groups, in general, demonstrate extensive heterogeneity and diverse genetic affinities with their geographic neighbors, suggesting a complex history, reflecting varying roles of migration from outside the Philippines, genetic drift, and admixture among FE groups and with other Asia-Pacific groups.” ref

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“Major East Eurasian ancestry lineages that contributed to modern human populations include the following:

• Australasian lineage — refers to an ancestral population that primarily contributed to human populations in a region consisting of Australia, Papua, New Zealand, neighboring islands in the South Pacific Ocean and parts of the Philippines. Represented by present-day Australasians, e.g. Papuans and Aboriginal Australians, as well as the Philippine Negritos.
• Ancient Ancestral South Indian lineage — refers to an ancestral population that primarily contributed to Indigenous South Asians. Partially represented by 5,000–1,500 year old Indus Periphery individuals as well as modern South Asians. Highest presence among tribal groups of southern India like the Paniya and Irula. While the lineage is occasionally represented by the distantly related Andamanese peoples, serving as an imperfect proxy, the Andamanese groups are genetically closer to the ‘Basal East Asian’ Tianyuan man.
• East and Southeast Asian lineage — refers to an ancestral population that primarily contributed to humans living in East and Southeast Asia, much of Remote Oceania, as well as Siberia and the Americas. Represented by ancient Tianyuan and Hoabinhian specimens and present-day East and Southeast Asians.” ref

“The Australasian, Ancient Ancestral South Indian, and East and Southeast Asian lineages display a closer genetic relationship to each other than to any non-Asian lineages and together represent the main branches of “Asian-related ancestry,” which diverged from each other >40,000 years ago. As such, we now know that the indigenous South Asians (AASI) formed their own branch of the wider East Eurasian lineage, and represent the South Asian-specific ancestry component. Now, we will take a closer look at the AASI lineage and its internal diversity and contact events: The AASI lineage forms a significant ancestral source for modern South Asian populations in terms of full genome and autosomal DNA makeup.” ref

In terms of uniparental haplogroups, the AASI contribution to modern South Asians is less clear, but we have some hints:

“Y-chromosome haplogroups which may be associated with AASI-like ancestry are the clades:

• H1 and H3
• K (K1 and K2)
• and C1″ ref

“The split of IJK* between IJ and K may be linked to the divergence of early West and East Eurasians, shortly before their dispersal waves from the Middle East. As K clades are nearly exclusively found among East Eurasians, deeply nested withing the AASI, Australasian, and ESEA groups, as well as among IUP remains, but absent from UP West Eurasians, it is plausible to see the local South Asian K subclades as possible AASI-affilated haplogroups, together with local C and D1 clades which were part of the ENA haplotype diversity (eg. C, D1, K branching off with Ancient East Eurasians).” ref

“Another possible candidate is haplogroup H, specifically the subclades of H1 and H3. H itself may have originated before the split of East and West Eurasians, as H2 is found mostly, althought at low frequency, among West Asians/Levantines and Europeans. Similarly, C1 is found in both West and East Eurasians, while C2 is solely found among ESEA-derived groups. This suggests that H and C were shared by the last common ancestor of West and East Eurasians some 50–55kya, together with IJK* and D1.” ref

“A possible correlation between haplogroups and autosomal DNA can be observed by looking at AASI-rich tribal groups. Here we find C1, K (both K1 and other K clades), and H1/H3 to be significantly higher than among caste and high caste populations. This may support either an AASI-affilation or later bottleneck events among them. In this regard, we will have to wait for actual AASI remains to be discovered and analysed, to know which haplogroups they carried. IMO a plausible candidate would be K and C1 clades and maybe H1/H3(xH2).” ref

“Note: It should be clear that haplogroups are not a good indicator of genetic divergence and overall ancestry. They make up a very small part of our total genome and can underwent strong drift and bottleneck events among different populations or groups. As such, carrying a specific haplogroup does not indicate a genetic link to a population with a high frequency of that haplogroup. Mt-DNA haplogroups associated with the AASI are mainly subclades of the Asian macro-haplogroup M. There are multiple subgroups. Like in the case of Y-DNA haplogroups, the Mt-DNA haplogroup does not give much information on the overall ancestry.” ref

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Haplogroup K-M9

“Y-DNA haplogroup K-M9 is an old lineage that arose approximately 47,000-50,000 years ago. According to geneticist Spencer Wells, haplogroup K or the Eurasian clan, originated in the Middle East (perhaps Iran) or Central Asia. Basal K* is exceptionally rare and under-researched; while it has been reported at very low frequencies on many continents it is not always clear if the examples concerned have been screened for subclades. Confirmed examples of K-M9* now appear to be most common amongst some populations in Island South East Asia and Melanesia. Primary descendants of haplogroup LT are L (M20), also known as K1a, and T (M184), also known as K1b.” ref

“The descendants of haplogroup K2 include:

• K2a (detected in paleolithic specimens Oase1 and Ust’-Ishim), the subclades of which include the major haplogroups N and O, and;
• K2b – the ancestor of haplogroups M, P, Q, R, S.” ref

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Haplogroup K2

“Haplogroup K2 Y-DNA and subclades of it are carried by males native to regions including Australasia, Oceania, Southeast Asia, South Asia, East Asia, Central Asia, the Americas, Europe, and the Horn of Africa.” ref

“Basal K2a* (K-M2308*) only in the remains of two Upper Paleolithic individuals, “Ust’-Ishim man” in Siberia and “Oase-1″ in the Banat region of south-central Europe, about 37,000–45,000 years ago.” ref

“Basal paragroup K2b* has not been identified among living males but was found in Upper Paleolithic Tianyuan man from China. K2b1, its subclades and P* are virtually restricted geographically to South East Asia and Oceania.” ref

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Ust’-Ishim man 45,000-year-old

Oase 1 man

Tianyuan man

Ust’-Ishim man

“Ust’-Ishim man is the term given to the 45,000-year-old remains of one of the early modern humans to inhabit western Siberia. The fossil is notable in that it had intact DNA which permitted the complete sequencing of its genome, one of the oldest modern human genomes to be so decoded. The remains consist of a single bone—left femur—of a male hunter-gatherer, protruding from the bank of the Irtysh River by Nikolai Peristov, a Russian sculptor who specialises in carving mammoth ivory. The fossil was named after the Ust-Ishimsky District of Siberia where it had been discovered.” ref

“Ust’-Ishim man belongs to Y-DNA haplogroup K2. The two subclades of K2 are K2a and K2b, and he has been found to be positive for some but not all SNPs of the K2a (or NO*) subclade, such as M2308. In the original paper, he was classified only as Haplogroup K-M9 (KxLT). He belonged to mitochondrial DNA haplogroup R*, differing from the root sequence of R by a single mutation. Both of these haplogroups and descendant subclades are now found among populations throughout Eurasia, Oceania and The Americas, although no direct descendants of Ust Ishim man’s specific lineages are known from modern populations.” ref

“Examination of the sequenced genome indicates that Ust’-Ishim man lived at a point in time between the first wave of anatomically modern humans (270,000 years ago) that migrated out of Africa and the divergence of that population into distinct populations (45,000 years ago), in terms of autosomal DNA in different parts of Eurasia. Consequently, Ust’-Ishim man is not more closely related to the first two major migrations of Homo Sapiens eastward from Africa into Asia: a group that migrated along the coast of South Asia, or a group that moved north-east through Central Asia. When compared to other ancient remains, Ust’-Ishim man is more closely related, in terms of autosomal DNA to Tianyuan man, found near Beijing and dating from 42,000 to 39,000 years ago; Mal’ta boy (or MA-1), a child who lived 24,000 years ago along the Bolshaya Belaya River near today’s Irkutsk in Siberia, or; La Braña man – a hunter-gatherer who lived in La Braña (modern Spain) about 8,000 years ago.” ref

“Analysis of modern human genomes reveals that humans interbred with Neanderthals between 86,000 and 37,000 years ago, resulting in the DNA of modern humans outside Africa containing between 1.5 and 2.1 percent DNA of Neanderthal origin. Neanderthal DNA in modern humans occurs in broken fragments; however, the Neanderthal DNA in Ust’-Ishim man occurs in clusters, indicating that Ust’-Ishim man lived in the immediate aftermath of the genetic interchange. The genomic sequencing of Ust’-Ishim man has led to refinement of the estimated date of mating between the two hominin species to between 52,000 and 58,000 years ago. No relationship between Denisovans and the Ust’-Ishim man has been checked, although Denisovans have some descendants in Oceania and Asia.” ref

“Ust’-Ishim was equally related to modern East Asians, Oceanians and certain ancient West Eurasian populations, such as the Goyet specimen. Modern Europeans are more closely related to other ancient remains. “The finding that the Ust’-Ishim individual is equally closely related to present-day Asians and to 8,000- to 24,000-year-old individuals from western Eurasia, but not to present-day Europeans, is compatible with the hypothesis that present-day Europeans derive some of their ancestry from a population that did not participate in the initial dispersals of modern humans into Europe and Asia.” ref

“In a 2016 study, modern Tibetans were identified as the modern population that has the most alleles in common with Ust’-Ishim man. According to a 2017 study, “Siberian and East Asian populations shared 38% of their ancestry” with Ust’-Ishim man. A 2021 study argues that the Ust’Ishim and Oase 1 individuals showed no more affinity to any modern western or eastern Eurasian populations, suggesting that they did not contribute ancestry to later Eurasian populations, as previously shown.” ref

“In 2022, a study determined that the Ust’Ishim man was part of an Initial Upper Paleolithic wave (>45,000 years ago) “ascribed to a population movement with uniform genetic features and material culture” (Ancient East Eurasians), and sharing deep ancestry with the Bacho Kiro, Oase and the Tianyuan man, as well as ancestors of modern-day Papuans (Australasians). The Ust’Ishim lineage is described as “near trifurcation” between West and East Eurasians, but sharing a short period of evolutionary drift with Eastern Eurasians, having diverged from their ancestor shortly after the divergence from Ancient Western Eurasians (represented by the Kostenki-14 specimen).” ref

Oase1 – Peștera cu Oase 

“Peștera cu Oase (meaning “The Cave with Bones”) is a system of 12 karstic galleries and chambers located near the city Anina, in the Caraș-Severin county, southwestern Romania, where some of the oldest European early modern human (EEMH) remains, between 42,000 and 37,000 years old, have been found. While “Oase 1” lower jaw is fully mature, the facial skeleton is that of a mid-second-decade adolescent, therefore corresponding to a second individual, designated as “Oase 2”. Further analyses have revealed that the left temporal bone represents a third individual, assessed as adolescent versus mature female, designated as “Oase 3.” ref

“However, additional finds and work have shown that the temporal bone derives from the same cranium as the “Oase 2” facial and parietal bones. The lack of archaeological signs such as torches, charcoal or tools could suggest that the human remains may have washed in the cave through fissures. The “Oase 2” and “Oase 3” confirm a pattern already known from the probably contemporaneous “Oase 1” mandible, indicating a mixture of archaic, early modern human and Neanderthal morphological features. Thus, the specimens exhibit a suite of derived “modern human” features like projecting chin, no brow ridge, a high and rounded brain case.” ref

“Yet, these features are associated with several archaic aspects of the cranium and dentition that place them outside the range of variation for modern humans, like a large face, a large crest of bone behind the ear and big teeth that get even larger toward the back. This mosaic of Neanderthal and modern human resembles similar traits found in a 25,000 years old fossil of a child in Abrigo do Lagar Velho or in the 31,000 years old site of Mladeč, by Cidália Duarte, et al. (1999). In 2015 genetics research revealed that the Oase 1 fossil had a recent Neanderthal ancestor, with an estimated 5-11% Neanderthal autosomal DNA. The specimen’s 12th chromosome was 50% Neanderthal.” ref

Oase 1

“In June 2003 a further research team with Ștefan Milota, Ricardo Rodrigo, and Mircea Gherase discovered additional human remains on the cave’s surface. Thus, an entire anterior cranial skeleton was found along with a largely complete left temporal bone and a number of frontal, parietal and occipital bone segments. The calibrated radiocarbon date for Oase1 is 40,450±1020 years ago. “Oase 1” exhibits morphological traits from early modern humans and archaic humans, including Neanderthal features.” ref

DNA analysis of Oase 1 since 2015 has made a number of significant findings:

• “About 6-9% of the genome is Neanderthal in origin. This is the highest percentage of archaic introgression found in an anatomically modern human and together with the linkage disequilibrium patterns indicates that Oase 1 had a relatively-recent Neanderthal ancestor – about four to six generations earlier.” ref
• “The autosomal DNA of Oase 1 by Fu et al. (2015) indicates that he (as it was a male) may have shared more alleles with modern East Asian populations than with modern Europeans. However, Oase shared equal alleles with Mesolithic Europeans and East Eurasians suggesting non pre LGM-European admixture in modern Europeans, part of it being from the Basal Eurasian ancestry that was carried to Europe by Anatolian farmers and Yamnaya pastoralists.” ref
• “Oase 1 belongs to an extinct Y-DNA haplogroup and an extinct mitochondrial DNA haplogroup.
  • Research by Poznik et al. (2016) suggests that Oase 1 Y-DNA belongs to haplogroup K2a*. That is, Oase 1 possesses SNPS similar to Ust’-Ishim man (also K2a*), 45,000-year-old remains from Siberia, and upstream from Haplogroup NO and a rare lineage found in two living males (from ethnic Telugu and Malay backgrounds, respectively, for whom Poznik et al. proposed the creation of a new subclade, named “K2a1”). (Earlier research by Fu et al. reported that Oase 1 belonged to a subclade of Y-DNA haplogroup F, other than haplogroups G, H, I and J – leaving open the possibility that Oase 1 belonged to macrohaplogroup K.)
  • According to Fu, Oase-1’s maternal lineage is related to mitochondrial DNA haplogroup N, but diverged from all other N clades before they diverged from each other.” ref

Oase 2

“Researchers sequenced the genome of “Oase 2” (41,500–39,500 years old) to high coverage (20-fold) from its petrous bone. Around 6% of “Oase 2″‘s genome is Neanderthal in origin, which is lower than for “Oase 1”; however, this is still much higher than expected based on its age and what is seen in other Upper Palaeolithic genomes. “Oase 2” belongs to the same basal subclade of mitochondrial DNA haplogroup N as “Oase 1”. When compared against all DNA samples on record, “Oase 2” and “Oase 1” share the closest genetic affinity with each other.” ref

“Oase 1” and “Oase 2″ appear to be from related, but not necessarily identical populations. “Oase 1” shows an affinity for Ice Age Europeans that is not found in “Oase 2”, while “Oase 2” is closer to Asians and Native Americans. “Oase 1” shows a genetic affinity for “Peştera Muierii 2” that is not found in “Oase 2”. After “Oase 1”, the next closest genetic affinity for “Oase 2” among ancient DNA samples is the c. 40kya Tianyuan man from Northern China. Neither “Oase 2” nor “Oase 1” are particularly close genetically to any modern human populations.” ref

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Tianyuan man

“Tianyuan man (simplified Chinese: 田园洞人; traditional Chinese: 田園洞人; pinyin: Tiányuándòng Rén) are the remains of one of the earliest modern humans to inhabit East Asia. In 2007, researchers found 34 bone fragments belonging to a single individual at the Tianyuan Cave near Beijing, China. Radiocarbon dating shows the bones to be between 42,000 and 39,000 years old, which may be slightly younger than the only other finds of bones of a similar age at the Niah Caves in Sarawak on the South-east Asian island of Borneo.” ref

“The first DNA analysis of the Tianyuan remains (focussing on mtDNA and chromosome 21) was published in 2013 and revealed that Tianyuan man is related “to many present-day Asians and Native Americans” and had already diverged genetically from the ancestors of modern Europeans. He belonged to mitochondrial DNA haplogroup B, and paternal haplogroup K2b. A genome-wide analysis confirmed the close affinity of Tianyuan man to modern East Asian and Southeast Asians, but also showed that he is not directly ancestral to modern populations, but rather represents a deeply diverged member of the East and Southeast Asian (ESEA) lineage, basal to all later populations of East and Southeast Asia.” ref 

“The Tianyuan man was determined to be part of an Initial Upper Paleolithic wave (>45,000 years ago) “ascribed to a population movement with uniform genetic features and material culture” (Ancient East Eurasians), and sharing deep ancestry with other ancient specimens such as Bacho Kiro, Peștera cu Oase, the Ust’-Ishim man, as well as the ancestors of modern day Papuans (Australasians). The lineage ancestral to the Tianyuan man (dubbed as the “ESEA” lineage) is inferred to have diverged from the Ancient East Eurasians, following a Southern Route dispersal, and subsequently diverged into the Hoabinhian lineage, the Tianyuan lineage, and a lineage ancestral to all modern East and Southeast Asians.” ref

“A Tianyuan-like population contributed around 32-50% ancestry to the Ancient North Eurasians, with the remainder being made up by Early West Eurasian ancestry represented by the Kostenki-14 specimen. A c. 34,000 year old specimen from Northern Mongolia (Salkhit) derives approximately 83% ancestry from a Tianyuan-like population, with the remainder (17%) being derived from a Kostenki14-like population. The Salkhit individual displayed a complex relationship to the Ancient North Eurasians.” ref

“Tianyuan man also exhibits a unique genetic affinity for GoyetQ116-1 from the Goyet Caves in Namur province, Belgium. GoyetQ116-1 shares more alleles with Tianyuan man than does any other sampled ancient individual from West Eurasia. The GoyetQ116-1 specimen is inferred to have received 14-23% ancestry from an Early East Eurasian population distantly related to the Tianyuan man. The Tianyuan man displays high genetic affinities to a 33,000 year old specimen (AR33K) between the Amur region and modern day Mongolia, suggesting that Tianyuan-like ancestry was widespreaded in Northeastern Asia during the Paleolithic period.” ref

“Basal East Asian or “Deep Asian” ancestry represented by Tianyuan or Andamanese Onge contributed to the Peopling of Southeast Asia, following Australasian ancestry and preceding Mesolithic and Neolithic expansions of Ancient Southern East Asians associated with the spread of Austroasiatic and Austronesian languages. The Tianyuan man also shares more alleles with South American populations, such as the Surui and Karitiana in Brazil and Chane in northern Argentina and southern Bolivia, than with other indigenous Americans.” ref

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“Hoabinhian is a stone tool-complex of archaeological sites associated with Southeast Asia from the late Pleistocene to the Holocene, dated to c. 10,000–2000 BCE.” ref

Extent of Hoabinhian technological tradition

Hoabinhian

“The Hoabinhian is a lithic techno-complex of archaeological sites associated with assemblages in Southeast Asia from the late Pleistocene to the Holocene, dated to c. 10,000–2000 BCE. It is attributed to hunter-gatherer societies of the region whose technological variability over time is poorly understood. In 2016, a rock shelter was identified in Yunnan, China, 40 km from the border with Myanmar, where artifacts belonging to the Hoabinhian technocomplex were recognized, dating from 41,500 BCE. The Bacsonian is often regarded as a variation of the Hoabinhian industry, characterized by a higher frequency of edge-grounded cobble artifacts compared to earlier Hoabinhian artifacts, dated to c. 8000–4000 BCE.” ref

“The oldest Hoabinhian complex was discovered at Xiaodong, a large rockshelter in Yunnan, China, 40 kilometres (25 mi) from the Burmese border. It is the only Hoabinhian site discovered in China. Archaeological sites in Terengganu, Sumatra, Thailand, Laos, Myanmar and Cambodia have been identified as Hoabinhian, although the quality and quantity of descriptions vary and the relative significance of the Hoabinhian component at these sites can be difficult to determine. Recent archaeological research indicates that variation in Hoabinhian artifacts across regions are largely influenced by local, region-specific proximity to resources and changes in environmental conditions. Beyond this core area, some archaeologists argue that there are isolated inventories of stone artifacts displaying Hoabinhian elements in Nepal, South China, Taiwan and Australia (Moser 2001).” ref

Pre-Hoabinhian technology

“Hà Văn Tấn outlined in his paper his definition of a lithic technology that occurred before the Hoabinian. He found primitive flakes in stratigraphy below Hoabinian pebble tools across several sites in Southeast Asia which led him to name the flake technology, Nguomian — named after a large assembly of flakes found at the Ngườm rock shelter in Thái Nguyên province, Vietnam. Hoabininhian technology is also claimed to be a continuation of the Sonvian technology.” ref

Hoabinhian and plant domestication

“Gorman (1971) claimed that Spirit Cave included remains of Prunus (almond), Terminalia, Areca (betel), Vicia (broadbean) or Phaseolus, Pisum (pea) or Raphia lagenaria (bottle gourd), Trapa (water caltrop), Piper (pepper), Madhuca (butternut), Canarium, Aleurites (candle nut), and Cucumis (a cucumber type) in layers dating to c. 9800-8500 BP. None of the recovered specimens differed from their wild phenotypes. He suggested that these may have been used as foods, condiments, stimulants, for lighting and that the leguminous plants in particular ‘point to a very early use of domesticated plants’ (Gorman 1969:672). He later wrote (1971:311) that ‘Whether they are definitely early cultigens (see Yen n.d.:12) remains to be established… What is important, and what we can say definitely, is that the remains indicate the early, quite sophisticated use of particular species which are still culturally important in Southeast Asia.” ref

“In 1972, W. G. Solheim, as the director of the project of which Spirit Cave was part, published an article in Scientific American discussing the finds from Spirit Cave. While Solheim noted that the specimens may ‘merely be wild species gathered from the surrounding countryside’, he claimed that the inhabitants at Spirit Cave had ‘an advanced knowledge of horticulture‘. Solheim’s chronological chart suggests that ‘incipient agriculture‘ began at about 20,000 BCE in southeast Asia. He also suggests that ceramic technology was invented at 13,000 BCE although Spirit Cave does not have ceramics until after 6800 BCE.” ref

Although Solheim concludes that his reconstruction is ‘largely hypothetical‘, his overstatement of the results of Gorman’s excavation has led to inflated claims of Hoabinhian agriculture. These claims have detracted from the significance of Spirit Cave as a site with well-preserved evidence of human subsistence and palaeoenvironmental conditions during the Hoabinhian. Viet (2004), however, focuses on mainly Hoabinhians in Viet Nam. Within his wide range of study of this area, Da But is a site that he has worked at which is dated to about fifth to sixth millennium BC to the end of the third millennium BCE. Within this site, Viet observed that the food Hoabinhians mostly focused on are mountainous shellfish, nuts, and fruit. Interesting enough, the site even shows a new shellfish species that they consumed: an as-yet-unnamed species of freshwater clam of Corbicula spp; species are known to live in swampy areas and lakes.” ref

“As of 2022, only two ancient DNA samples have been extracted from individuals excavated in Hoabinhian contexts: one specimen from in Pha Faen in Bolikhamxay Province, Laos (7,888 ± 40 years ago) and one from Gua Cha in Ulu Kelantan, Malaysia (4,319 ± 64 years ago). While the Upper Paleolithic origins of this Hoabinhian ancestry represented by the two samples are unknown, Hoabinhian ancestry has been found to be related to the main ‘East Asian’ ancestry component found in most modern East and Southeast Asians, although deeply diverged from it. Among present-day populations, the Andamanese Onge and Jarawa, and the Semang (also known as “Malaysian Negritos“) and Maniq in the interior of the Malay Peninsula are genetically closest to the sampled ancient Hoabinhian individuals.” ref

“The emergence of the Neolithic in Southeast Asia went along with a population shift caused by migrations from southern China. Neolithic Mainland Southeast Asian samples predominantly have East Asian ancestry related to ancient populations from southern China, but many of these samples also display admixture with Hoabinhian-related ancestry to a smaller degree. In modern populations, this admixture of East Asian and Hoabinhian-related ancestry is most strongly associated with Austroasiatic-speaking groups, and can also be reproduced in models where Onge samples are taken as proxies for Hoabinhian ancestry.” ref

Sequence analyses of Malaysian Indigenous communities reveal historical admixture between Hoabinhian hunter-gatherers and Neolithic farmers

“Abstract: 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.” ref

“Southeast Asia 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 Southeast Asia dates back to around 70,000–50,000 years ago. 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, Papua New Guinea, and Australia. Subsequently, migrations from East Asia during the late-Pleistocene and Holocene, and population movements within the region, have shaped today’s population structure of Southeast Asia. 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 Southeast Asia.” ref

“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.” ref

“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 Orang Asli tribe group is further subdivided into 6 subgroups, which makes up 18 Orang Asli tribe 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.” ref

“Early anthropological studies proposed multiple competing theories about the origin of Orang Asli tribes. The “layer-cake” theory postulated that all three Orang Asli tribe 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 Orang Asli tribes 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 5,000–7,000 years ago.” ref

“Early mtDNA studies found both haplogroups unique to Peninsular Malaysia, and those stablished in Indochina in Orang Asli tribes  which suggest gene flow from neighboring populations in SEA into Orang Asli tribes . These studies identified two haplogroups of M21 and R21 in Negrito and Senoi with TMRCA around 30,000–50,000 years ago. 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 East Asia compared with the other two Orang Asli tribe groups. This study also traced some level of gene flow from South Asia in Orang Asli tribes.” ref

“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. Principal Component Analysis comparing indigenous populations of Malaysia with worldwide populations from the HGDP-CEPH dataset revealed that the indigenous Malaysians are genetically close to East Asian populations. This suggests shared ancestors with East Asia or considerable gene flow between the two groups. On a finer scale, using populations from East, South, and Southeast Asia, Orang Asli tribes especially the Malaysian Negritos, exhibit an affinity towards the South Asians and Andamanese groups, while Dusun from North Borneo cluster closer to the East Asians.” ref

“This implies a possible admixture between Orang Asli tribes and South Asians. To explore the relation of Malaysian Negritos with Hoabinhian hunter-gatherers and southeast Asian early farmers we carried out a Principal Component Analysis using ancient Southeast Asia samples. The ancient Southeast Asia dataset we used in this study includes two Hoabinhian individuals (La368 and Ma911) as well as several Neolithic farmers discovered in archeological sites across Malaysia, Vietnam, Laos and Thailand. Principal Component Analysis with ancient Southeast Asia shows that the ancient samples belonging to the Hoabinhian culture cluster adjacent to the modern-day Andamanese. Malaysian Negritos positioned intermediate between the Andamanese/Hoabinhian and East Asia clusters while the rest of Orang Asli tribes were closer to Neolithic Southeast Asia. We conducted ADMIXTURE analysis to infer the genetic ancestry of Orang Asli tribes. The Malaysian Negritos displayed a mixture of Southeast Asia, Andamanese, and South Asians components.” ref

Y-chromosome and mitochondrial DNA haplogroup analysis

“We determined the Y-chromosome and mitochondrial DNA haplogroups in the OAs and North Bornean samples. For mtDNA, we observed five haplogroups including R21, M21a, M13b1, M17a, and F1a1a in Malaysian Negritos. MahMeri harbored the N22a haplogroup. Jakun carried the E1a2 haplogroup, while all Seletar carried N9a6b. We found two different haplogroups, M7c1c3 and R9c1a, in the Dusuns. The TMRCAs of the R21, M21a, M17a, and F1a1a haplogroups have been dated to 23,000, 19,000, and 8,000 years ago, respectively, and have previously been reported In Malaysian and Thai hunter-gatherers. Haplogroup M13b has been dated to around 31,000 years ago and observed in low frequency in Asia, specifically in Malaysia, Tibet, and Nepal. The N9a haplogroup is widespread in East Asia, SA, and SEA.” ref

“However, its sub-clade N9a6 appears limited to mainland Southeast Asia (MSEA) and reaches the highest frequency in Peninsular Malaysia. 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. The E1a, M711, R9c1 haplogroups are prevalent in island Southeast Asia and are widely believed to be associated with the Austronesian expansion. For the Y chromosome, Orang Asli 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 Southeast Asia, Negritos, and Oceania. Interestingly, we found haplotypes R2a and R1a1ab in Malaysian Negrito. Haplogroup R2a is mainly present in South Asia and at lower frequencies in Central, Southwest, and East Asia, while the R1a1a1b, and its sub-clades, comprise the major R1a sub-clades in Central and South Asia.” ref

“In general, Orang Asli tribes retained a lower Ne after around 30,000 years ago than neighboring populations. These results could be further supported by the runs of homozygosity (ROH) analysis which revealed long stretches of ROH in Orang Asli tribes. We found an increase in Ne in Dusun around 6,000 years ago, which possibly coincides with the Austronesian expansion. For the divergence time, we found that the split between Malaysian Negritos and EA took place around 14–13,000 years ago which is consistent with the results of our previous study using genotyping data. Seletar and Dusun diverged from Han around 10 kya, which is in good agreement with the initial divergence of Austronesian from EA44. Overall, the divergences between different Malaysian groups were relatively recent. The divergence between Malaysian Negritos and Austronesians occurred around 12,000 years ago, followed by a split from MahMeri around 9,000 years ago. Jehai and Mendriq (two Negrito tribes) separated from each other approximately 2,600 years ago.” ref

Gene flow between indigenous Malaysian and neighboring populations

“The tree topology revealed that Malaysian Negritos formed a separate cluster while the other Malaysian indigenous groups clustered with EA populations. We identified gene flow between Andamanese and Malaysian Negritos. Our analysis also demonstrated gene flow between Dusun and Melanesian Bougainville. This may reflect the admixture between a population genetically close to today’s Dusun in Borneo and a population with Papuan ancestry, attributed to the Austronesian expansion, which has been described by previous studies. We also detected gene flow within Orang Asli tribe groups, notably from Jehai (Negrito) to Jakun (Proto-Malay), and from MahMeri (Senoi) to Mendriq (Negrito).” ref

“Malaysia which lies at the crossroads of South East Asia, has experienced multiple massive human movements over millennia. Archeological and genetic evidence shows that the presence of AMH in Malaysia dates back to at least 40,000 years ago. Between 13,000 to 3,000 years ago 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 4,000 years ago, this South East Asian nation also witnessed at least two waves of migration from Neolithic farmers and Austronesian speakers. These different human migrations and settlements have resulted in Malaysia’s rich present-day linguistic and anthropological diversity. Our study leverages new whole-genome sequencing data to dive deeper into the understanding of the genetic structure and history of the indigenous people of this nation.” ref

“While indigenous Malaysians are genetically closer to East Asian populations, consistent with previous studies, our new ADMIXTURE analysis revealed traces of South Asian ancestral component in Orang Asli tribes of Peninsular Malaysia. We could not detect this component in Dusun in Borneo. The presence of South Asian ancestral component in Orang Asli tribes has been previously reported. This ancestral component might be attributed to the first wave of human migration into South East Asian via the southern coastal route or later gene flow from South Asian during the expansion of Indian culture into Peninsular Malaysia in the first century CE. 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. More studies are needed to address the source of South Asian ancestry in Peninsular Malaysia and its absence in Borneo.” ref

“Analysis of Orang Asli tribes 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 9,000 years ago and later the Neolithic farmers used this site from 3,000 years ago. 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.” ref

“Our analysis detected gene flow between different Orang Asli tribes, notably between Malaysian Negritos, with MahMeri and Jakun tribes. The admixture between neighboring Orang Asli tribes or between Orang Asli tribes 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.” ref

“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. In summary, our study suggests that at least 3 ancestral components were involved in shaping today’s indigenous Malaysian populations, the Hoabinhian hunter-gatherers, Neolithic farmers, and Austronesian speakers. We also showed the genetic interaction between different Orang Asli tribes of Peninsular Malaysia.” ref

Orang Asli tribes

“Orang Asli are a heterogeneous indigenous population forming a national minority in Malaysia. They are the oldest inhabitants of Peninsular Malaysia. As of 2017, the Orang Asli accounted for 0.7% of the population of Peninsular Malaysia. Although seldom mentioned in the country’s demographics, the Orang Asli are a distinct group, alongside the Malays, Chinese, Indians, and the indigenous East Malaysians of Sabah and Sarawak. Their special status is enshrined in law. Orang Asli settlements are scattered among the mostly Malay population of the country, often in mountainous areas or the jungles of the rainforest.” ref

“While outsiders often perceive them as a single group, there are many distinctive groups and tribes, each with its own language, culture and customary land. Each group considers itself independent and different from the other communities. What mainly unites the Orang Asli is their distinctiveness from the three major ethnic groups of Peninsular Malaysia (ethnic Malays, Chinese, and Indian) and their historical sidelining in social, economic, and cultural matters. Like other indigenous peoples, Orang Asli strive to preserve their own distinctive culture and identity, which is linked by physical, economic, social, cultural, territorial, and spiritual ties to their immediate natural environment.” ref

“Prior to the official use of the term “Orang Asli” beginning in the early 1960s, the common terms for the indigenous population of Peninsular Malaysia varied. Thomas John Newbold recorded that “Malays” of Rembau in present-day Negeri Sembilan had given their local forest-dwelling hunter-gathering population the contemporary name of orang benua (Jawi: اورڠ بنوا‎) meaning “people of the soil or country”. Towards the end of British colonial rule on the Malay Peninsula, there were attempts to classify these disparate groups. Residents of the southern regions often called them Jakun, and those in the northern regions called them Sakai. Later on, all indigenous groups became known as Sakai, meaning Aborigines.” ref

“The term “aborigines”, as an official name, appeared in the English version of the Constitution of British Malaya and the laws of the country. Past colonial rule by European and Islamic powers gave both the Malay word Sakai and the English term Aborigines pejorative connotations, hinting at the supposed backwardness and primitivism of these people. During the Malayan Emergency in the 1950s Communist rebels, seeking the support of the indigenous tribes, began referring to them as Orang Asal, meaning “native people”: asl “origin”. The Communists won their support, and the government, seeking to do the same, began adopting the same terminology. Thus, the new, slightly modified term “Orang Asli”, carrying the same sense of “original people”, was born. The term was officially used in English, where it is identical in both the singular and the plural. Despite its origin as an exonym, the term was adopted by indigenous peoples themselves.” ref

“The Orang Asli makes up one of 95 subgroups of indigenous people of Malaysia, the Orang Asal, each with their own distinct language and culture. The British colonial government classified the indigenous population of the Malay Peninsula on physiological and cultural-economic grounds upon which the Aboriginal Department (responsible for dealing with Orang Asli issues since the British Malaya government) developed their own classification of indigenous tribes based on their physical characteristics, linguistic kinship, cultural practices and geographical settlement. This divides Orang Asli into three main categories, with six ethnic subgroups each (totaling 18 ethnic subgroups).” ref

• “Negrito (or Semang), generally located in the northern portion of the peninsula, were short dark-skinned nomadic hunter-gatherers with Asiatic facial features and tightly curly hair.
• Senoi (or Sakai), residing in the central region, were wavy-haired people taller than the Negrito, engaged in slash-and-burn agriculture, and periodically changed their place of residence.
• Proto-Malay (or Aboriginal Malay), living in the southern region, were settled farmers, lighter-skinned, of normal height, with straight hair.” ref

“This division does not claim to be scientific and has many shortcomings. The boundaries between the groups are not fixed, and merge into each other, and the Orang Asli themselves use names associated with their specific area or by a local term meaning ‘human being’. Semang are part of the earliest modern human migration that arrived Peninsular Malaysia 50 to 60 thousand years ago, while Senoi are part of Austroasiatic population that arrived Peninsular Malaysia 10,000 to 30,000 year ago. Some earlier hypotheses pointed out the Semang and Senoi as descendants of the Hoabinhian people, Further research showed Semang shared genetic drift with ancient genomes from Hoabinhian ancestry, suggesting that they are genetically closer to the ancestors of Hoabinhian hunter-gatherers who occupied northern parts of Peninsular Malaysia during the late Pleistocene. Both groups speak Austroasiatic languages (also known as Mon-Khmer language).” ref

“The Proto-Malays, who speak Austronesian languages, migrated to the area between 2000 and 1500 BCE during the Austronesian expansion. Along with the ethnic Malays, they originated from the seaborne migration of the Austronesian peoples, ultimately from Taiwan. It is believed that Proto-Malays were the first wave of Proto-Malayo-Polynesian speakers that settled Borneo and the western Sunda Islands initially, but didn’t penetrate Peninsula Malaysia due to preexisting populations of Austroasiatic speakers. Later Austronesian migrations from either western Borneo or Sumatra, settled the coastal areas of Peninsular Malaysia became the modern Malayic-speaking populations (“Deutero-Malays”). However, other authors have also concluded that there is no real distinction between Proto-Malays and Deutero-Malays, and both are descendants of a single migration event into Sumatra, Peninsular Malaysia and southern Vietnam from western Borneo, This migration diverged into the modern speakers of the Malayic and Chamic branches of the Austronesian language family.” ref

“The Proto-Malays were originally considered ethnic Malay, but reclassified arbitrarily as part of Orang Asli by the British colonial authorities due to the similarity of their socio-economic and lifestyles with the Senoi and Semang. There are various degrees of admixture within all three groups. Only over time did indigenous peoples begin to identify themselves under the common name “Orang Asli” as a marker of collective identity as natives, distinct from the predominant ethnic groups more recently arrived to the peninsula. Orang Asli seldom associate themselves with the categories of “Negrito”, “Senoi” and “Aboriginal Malays.” ref

“The Orang Asli Negrito share a common genetic origin with East Asian people, but each can be differentiated on a finer scale. According to the Encyclopedia of Malaysia, the Semang or Pangan are regarded as the earliest inhabitants of the Malay Peninsula. They live mainly in the northern regions of the country, and are considered to be mostly descended from the people of the Hoabinhian cultural period, with many of their burials found dating back 10,000 years ago. They speak the Aslian languages branch of the Mon-Khmer language which is part of the Austroasiatic language family, as do their Senoi agriculturalist neighbours. Most of them belong to the North Aslian language group, and only the Lanoh language belongs to the Central Aslian languages group.” ref

First settlers

“The earliest traces of modern humans in the Malay Peninsula, archaeologists date back to a period of about 75,000 years ago. Next, a number of evidence of ancient people living in the north of the peninsula were left about 40,000 years ago. The climate and geography of Southeast Asia at that time were vastly different from today. During the Ice age period, the sea level was much lower, the seabed between the islands of the Sunda archipelago was then land, and the Asian mainland extended to present-day Sumatra, Java, Bali, Kalimantan, Palawan, forming the so-called Sundaland.” ref

“Global warming about 10,000 years ago caused glacier melt and rising sea levels resulting in the formation of the Malayan peninsula by approximately 8,000 years ago. It is believed that the surviving prehistoric population were the ancestors of today’s Semang people. Recent genetic studies identify them as a relic group of people who are descendants of the first migrants who came from Africa between 44,000 and 63,000 years ago.  This does not mean, however, that they have survived to this day in their original form. Over thousands of years, they have undergone local evolution. Thus, the Hoabinhian inhabitants of the Malay Peninsula were taller than the modern Semang people and did not belong to the Negrito race. Recent studies have also shown genetic differences between Semang people and other Negritos, such as the indigenous Andamanese peoples and those from the Philippine Islands.” ref

“Evidence of early human occupation of the Peninsula includes prehistoric artefacts and cave paintings such as the Tambun rock art, which is estimated to be around 2,000 to 12,000 years old. About 6,000–6,500 years ago, climatic conditions stabilized. This period is marked by the appearance of the Neolithic on the Malay Peninsula, which is associated with the archaeological culture of Hòa Bình. New groups of people genetically related to the population of Thailand, Cambodia and Vietnam arrived on the Malay Peninsula bringing new technologies, better tools, and ceramics. In the peninsula, slash-and-burn agriculture was commonly practiced. Traditionally, these migrants are associated with the ancestors of the Senoi people, but genetic studies suggest that the influx of new population was small, and migrants were mixed with locals.” ref

“According to Glottochronology data, speakers of Aslian languages appeared in the Malay Peninsula, dating from about 3,800 to 3,700 years ago. This is consistent with the peninsula ceramic tradition of Ban Kao from Central Thailand. During 2,800–2,400 years ago, the differentiation of the North Aslian language, Central Aslian languages and Southern Aslian languages began to develop.” ref

Early history

“Some groups of the Austronesian speakers began to arrive in the Malay Peninsula, probably from Kalimantan and Sumatra, in 1000 BCE. According to linguists, some of these early non-Malay arrivals are of Malayo-Polynesian peoples. These Proto-Malay tribes inhabited mostly small, geographically divided groups along the coast and along rivers, while the inner jungle areas remained entirely with the native population. Each group of Proto-Malays developed their local character, adapting to specific local conditions. The Southern Aslian speakers had the greatest contact with the newer population. It is believed that the ancestors of Jakun people and Temuan people who now speak Malay language, were native speakers of Aslian in the past.” ref

“The Orang Asli kept to themselves until the first traders from India arrived in the first millennium of the Common Era. Maritime trade routes brought traders from India, China, the Mon kingdoms located in modern-day Myanmar, and later from the Khmer Empire of Angkor, in search of local produce. Those living in the interior bartered inland products like resins, incense woods, and feathers for salt, cloth, and iron tools. From about 500 BCE or 2,500 years ago, on the west coast of the Malay Peninsula and on either side of the Kra Isthmus, traders established their settlements, some of which later grew into large trading ports. At that time Kedah, in particular, was becoming an important center of international trade.” ref

The emergence of the Malays

“The development of the slave trade in the region was a powerful factor influencing the fate of the Orang Asli. The enslavement of Negrito tribes commenced as early as 724 CE, during the early contact of the Malay Srivijaya empire. Negrito pygmies from the southern jungles were enslaved, with some being exploited until modern times. Because Islam prohibited taking Muslims as slaves, slave hunters focused their capture on the Orang Asli explaining the Malay use sakai to mean “slaves” with its present derogatory connotation. In the early 16th century Aceh Sultanate, located in the north of the island of Sumatra, equipped special expeditions to capture slaves in the Malay Peninsula, and Malacca was at that time the largest center of the slave trade in the region.” ref

“Raids on slaves in the villages of Orang Asli were common in the 18th and 19th centuries. During this time, Orang Asli groups suffered raids by the Minangkabau and Batak forces who perceived them to be of lower in status. Orang Asli settlements were sacked, with adult males being systematically executed while women and children were taken captive and sold into slavery. Hamba abdi (meaning, bondslaves) formed the labour force both in the cities and in the households of chiefs and sultans. They could be servants and concubines of a rich master, and slaves also did labour work in commercial ports.” ref

“However, the relationship between the Malays and Orang Asli was not always hostile, as many other groups enjoyed peaceful and cordial relation with their Malay neighbors. With the easement of mobility and contact between various groups of people, the walls that separated the myriad of historical Austroasiatic and Austronesian tribal communities who once dwelled across the peninsula were dismantled, being gradually drawn and integrated into the Malay society, identity, language, culture and belief system. These Malayised tribes and communities would later be part of the ancestors of present-day Malay people.” ref

“The new situation prompted many Orang Asli to migrate further inland to avoid contact with outsiders. These other smaller, closely related tribes; often located further inland compared to their coastal Malayized cousins, managed to be spared from the Malayization process due to their secluded geographical location and nomadic and semi-nomadic lifestyle, hence preserving and developing their own endemic language, customs and pagan rituals. As the Malays advanced into the country, the Orang Asli slowly retreated further and further, concentrating mainly in the foothills and mountains.” ref

“They were fragmented into small isolated tribal groups that occupied certain ecological niches, such as the river valley and had limited contact with neighboring outsiders. Malay settlements were usually located on the coast or along rivers, as the Malays rarely crossed into the interior jungles. Nevertheless, some Orang Asli groups not completely isolated from their Malayalized brothers engaged in trade with the Malays. A minority of Orang Asli rejected assimilation including the indigenous tribes of the Malay Peninsula as well as the Orang Kanaq or the Orang Seletar who refused Islam.” ref

“The way of life and management of certain groups of Orang Asli differs markedly. There are three main traditions that existed in the past, the nomadic hunter-gatherers Semangs, the settled population engaged in slash-and-burn agriculture Senois, and settled farmers who additionally collect jungle produce for sale Proto-Malays. Each of these traditions corresponds to a certain social structure of society. About 40% of Orang Asli, including the Temiar people, Cheq Wong people, Jah Hut people, Semelai people, and Semaq Beri people, continue to live in or near jungles. Here they are engaged in slash-and-burn agriculture (growing Upland rice on the hills), as well as hunting and gathering.” ref

“In addition, these communities sell foraged jungle resources (petai, durian, rattan, wild rubber) in exchange for money. Coastal communities (Orang Kuala, Orang Seletar and Mah Meri people) are mainly engaged in fishing and seafood harvesting. Others, including Temuan people, Jakun people and Semai people, are constantly engaged in agriculture, and now also have their own plantations for growing rubber, oil palm and cocoa. Very few Orang Asli, especially among Negrito groups (such as the Jahai people and Lanoh people), still lead a semi-nomadic lifestyle and prefer to enjoy the seasonal bounties of the jungle. Many Orang Asli also lives in cities where they work as hired workers.” ref

“Nomadic groups, such as the Jahai people and Batek people, live in families that occasionally gather together in temporary camps and then separate from each other again, but to reunite in a new camp and in a different composition. Some agricultural groups, such as the Temiar people, are organised into extended families and small groups linked by a common origin. They trace their descent from a common ancestor along both male and female lineages.” ref

“The Semang and Senoi ethnic groups are politically and socially egalitarian, where everyone in the community is completely autonomous. If they have their leaders, they exercise only temporary situational power, which is based solely on the personal authority of a certain person. Such a leader has no real authority. At the same time, some southern groups, including the Semelai people, the Jakun people, and the Temuan people, had their own hereditary batin (meaning, village head) leaders in the past.” ref

“All Orang Asli consider their customary territories to be free for gathering by all members of the community. In some groups, individual families have exclusive rights to the agricultural land they cultivate, which they have cleared from the jungle on their own. However, when such a field is abandoned and overgrown with jungle, it returns to the common property of the whole community. One remarkable feature of Orang Asli communities is that they prohibit any interpersonal violence, both within their groups and in relationships with outsiders. Their survival strategy has traditionally been to avoid contact with the country’s dominant populations, and they teach their children to refrain from all forms of violence.” ref

“The rules governing marriage differ from one tribe to another Orang Asli. In Semangs, social structures are adapted to the nomadic way of life of hunter-gatherers. They are forbidden to marry and have intimate relations with blood or related relatives through marriage. These rules of exogamy require one to look for a spouse among distant groups, thus creating a wide network of social ties. The tradition of Senoi is associated with the practice of slash-and-burn agriculture. Their local groups are more stable than those of the Semangs, therefore the prohibition of marriages between relatives is not so strict, as a result, family ties are concentrated within a certain river valley.” ref

“The Malay tradition is associated with a sedentary lifestyle, so Malays and Aboriginal Malays prefer to marry within a village or locality, and marriages between cousins are allowed. This practice of local endogamy strengthens people’s commitment to their own economic system and keeps them from accepting other traditions. Such differences in views on the rules of marriage allowed for several thousand years to coexist side by side and not to intermarry with groups with very different economic complexities.” ref

“Traditional Orang Asli religions consist of complex systems of beliefs and worldviews that give these people the concept of the meaning of the world, the meaning of human life, and the moral code of conduct. Orang Asli is traditionally animists, where they believe in the presence of spirits in various objects. It allows the indigenous people to be in constant harmony with the natural environment. Most Orang Asli believes that the universe consists of three worlds, namely the celestial upper world, the terrestrial middle world, and the subterranean lower world. All three worlds are inhabited by various supernatural beings (spirits, ghosts, deities), which can be both helpful and harmful to humans. Some of these supernatural beings are individualised entities that have their own names and are associated with specific natural phenomena, such as thunderstorms, floods, or fruit ripening. Most Orang Asli believes in the “God of Thunder”, who will punish people by sending them a terrible storm.” ref

“Traditional Orang Asli rituals are designed to maintain a harmonious relationship between humans and supernatural beings. They offer sacrifices to the spirits, praise and gratitude, ask permission to kill animals during hunting, cut down trees, plant cultivated plants, and ask for abundant harvests of wild fruits. More complex rituals are performed by shamans, many of whom have their own spiritual guides in the spirit world. Most of these people believe that spells can cure diseases or ensure success in any field of activity, usually with the help of supernatural beings. During those ritual sessions, the shaman falls into a trance, and his soul goes to travel the worlds, looking for the lost souls of sick people, or meets with supernatural beings and asks them for help.” ref

“However, in the 21st century, many of them have also embraced monotheistic religions such as Islam and Christianity following some active state-sponsored dakwah by Muslims, and evangelism by Christian missionaries. Pahang Islamic Religious and Malay Customs Council (Majlis Ugama Islam Dan Adat Resam Melayu Pahang, MUIP) filed new Orang Asli Muslim converts from Pahang in 2015 alone. On June 4, 2007, an Orang Asli church was allegedly torn down by the state government in Gua Musang, Kelantan. In January 2008, a suit was filed against the Kelantan state authorities. The affected Orang Asli also sought a declaration under Article 11 of the Constitution of Malaysia that they have the right to practice the religion of their choice and to build their own prayer house. A major scandal involving the deaths of several escapee Orang Asli students led to a discussion over the role of religious indoctrination in schools and forced conversion of Orang Asli community to Islam by the state government.” ref

“The lifestyle of certain Orang Asli groups that were formed for many centuries, has resulted in the way of solving practical problems and opportunities that these people faced in specific natural and social conditions. Orang Asli communities demonstrate how social life can be reconciled without a hierarchical political system as an intermediary, but instead with gender equality, a combination of close cooperation and mutual assistance with personal autonomy.” ref

“Some of their methodology, which the Orang Asli themselves take for granted, seems to gain the attention of Westerners. Andy Hickson and his mother, Sue Jennings, after living in the Temiar community for more than a year, not only appreciated the nation’s social heritage but also began to apply it in their practice. Andy Hickson, who works as a consultant in the education system, began to use interactive methods of Temiar people in the fight against the phenomenon of intimidation of students. Therapist Sue Jennings applies aspects of the Temiar ritual traditions in her group therapy sessions.” ref

Genetics of South Asia, Andamanese peoples, Indus Valley Civilization, Peopling of India, Dravidian languages, and the Paliyan/Pulliyar Dravidian tribal people