The Demographic History Of Southeast Asia

Analysis of uniparental DNA clades and linguistic evidence in modern Southeast Asian populations and archaeology had supported this conclusion a decade ago. The migrationist paradigm continues to rule. Now, ancient DNA confirms it. 

Two distinct population models have been put forward to explain present-day human diversity in Southeast Asia. The first model proposes long-term continuity (Regional Continuity model) while the other suggests two waves of dispersal (Two Layer model). 

Here, we use whole-genome capture in combination with shotgun sequencing to generate 25 ancient human genome sequences from mainland and island Southeast Asia, and directly test the two competing hypotheses. 

We find that early genomes from Hoabinhian hunter-gatherer contexts in Laos and Malaysia have genetic affinities with the Onge hunter-gatherers from the Andaman Islands, while Southeast Asian Neolithic farmers have a distinct East Asian genomic ancestry related to present-day Austroasiatic-speaking populations. 

We also identify two further migratory events, consistent with the expansion of speakers of Austronesian languages into Island Southeast Asia ca. 4 kya, and the expansion by East Asians into northern Vietnam ca. 2 kya. These findings support the Two Layer model for the early peopling of Southeast Asia and highlight the complexities of dispersal patterns from East Asia.

Hugh McColl, et al., "Ancient Genomics Reveals Four Prehistoric Migration Waves into Southeast Asia" BioRxiv (March 8, 2018).

Some first blush thoughts.

Two(+2) early waves or three (+2)?

Was there are distinct pre-Hoabinhian wave of pre-Papuan/Australian folk whom Onge-like hunter-gatherers (largely) replaced? If there was a replacement, what gave the newcomers an edge and when did that replacement happen?

The first paragraph of the paper impliedly raises this question but it doesn't seem to get resolved. It says:

The population history of Southeast Asia (SEA) has been shaped by interchanging periods of isolation and connectivity. Anatomically modern humans first colonized SEA at least 70,000 years ago. Within SEA, the complex topography and changes in sea level promoted regional expansions and contractions of populations. By the late Pleistocene/early Holocene, a pan-regional lithic technological culture was established across mainland SEA, named Hoabinhian. Hoabinhian foragers are thought to be the ancestors of present-day SEA hunter-gatherers, sometimes referred to as ‘Negritos’ because of their comparatively darker skin colour and short stature. Today, however, the majority of people in SEA are believed to be descendants of rice and millet farmers with varying degrees of East Asian phenotypic affinity, suggesting that human diversity in SEA was strongly influenced by population expansions from the north. Yet, the extent to which the movements from East Asia (EA) impacted on the genetic and cultural makeup of the people of SEA remains controversial.

The early Holocene is 10,000 years ago, leaving a 60,000 year gap between the first settlers and the Hoabinhian culture. There are limits to what the ancient DNA can do to resolve this because the ancient DNA samples in the study are not too old (the oldest is no more than 8,000 years old at more than two sigma). But, on closer examination, it appears that this question was examined but not resolved.

Unlike all other ancient samples, the two Hoabinhian samples (which also happen to be the oldest samples in our study) - Pha Faen, Laos (La368 - 14 140 C 7,888 ± 40) and Gua Cha, Malaysia (Ma911 - 14 C 4,319 ± 64) - designated as Group 1, cluster distantly from most East and Southeast Asians in the PCA and position closely to present-day Onge (Figure 1A). Group 1 individuals also contain a mixture of several different ancestral components in the fastNGSadmix plot, including components shared with Onge, the Pahari and Spiti from India, Papuans and Jehai (a Malaysian ‘Negrito’ group), which are markedly different from the other SEA ancient samples. This possibly results from our modeling of ancient populations as a mixture of components inferred in present-day populations, via fastNGSadmix, and from the fact the ancient samples are likely poorly represented by a single present-day group. 

The rest of the ancient samples are defined primarily by East and Southeast Asian components that are maximised in present-day Austroasiatic (Mlabri and Htin), Austronesian (Ami) and Hmong (indigenous to the mountainous regions of China, Vietnam, Laos and Thailand) populations, along with a broad East Asian component. . . . 

We used D-statistics of the form D(Papuan,Tianyuan,X,Mbuti), where X is a test population, to explore the relatedness of ancient and present-day Southeast Asians to two highly differentiated groups: Papuans and an ancient northern East Asian individual (Tianyuan - a 40 kya-old sample from Northeastern China). The values of this D-statistic are consistent with present-day and ancient SEA mainland samples being more closely related to Tianyuan than to Papuans. This applies to present-day northern EA populations, and - more weakly - to most populations of ancient and present-day SEA. However, this D-statistic is not significantly different from 0 in present-day Jehai, Onge, Jarawa and Group 1 - the ancient Hoabinhians. While the Onge’s relationship with Papuans and Tianyuan is unclear, D-statistics of the form D(Onge,Tianyuan,X,Mbuti), where X is a test population, show that Jarawa, Jehai and the ancient Group 1 share more ancestry with Onge than with Tianyuan. Like the Onge, both Group 1 samples carry mtDNA haplogroups from the M lineage, thought to represent the coastal migration to Australasia. 

To assess the diversity among the remaining ancient individuals, we computed a new PCA including only EA and SEA populations that did not have considerable Papuan or Ongelike  ancestry. . . . 

Group 2 samples from Vietnam, Laos, and the Malay Peninsula are the oldest samples after Group 1, and range in age from 4.2 to 2.2 kya. 

At K=6, Group 2 individuals, the present-day Mlabri and a single Htin individual are the only MSEA samples in the fastNGSadmix analysis to lack the broad EA component (dark green) maximised in northern EA , with the exception of the Malaysian ‘Negritos’ and ‘Proto-Malays’ (Temuan). 

At K=7, a bright green component is maximised in these populations, and this component is also found in present-day Indonesian samples west of Wallace’s Line. The two ancient Indonesian samples (Group 5; 2.2 to 1.9 kya) represent a mix of Austronesian- and Austroasiatic-like ancestry, similar to present-day western Indonesians. Indeed, after Mlabri and Htin, the closest populations to Group 2 based on outgroup-f3 statistics are the western Indonesian samples (from Bali and Java) reported to have the highest amounts of ancestry from mainland SEA. 

These lines of evidence suggest Group 2 are possible descendants of an “Austroasiatic” migration that expanded southward across MSEA and into island SEA (ISEA) by 4 kya. We also observe a gradient in “Austronesian-like” vs. “Austroasiatic-like” ancestry in the PCA: while PC1 separates populations found in SEA and those found in northern EA, PC2 distinguishes population based on their amounts of Austronesian-like ancestry (pink component in Figure 1 - lower panel) versus Austroasiatic-like ancestry (bright green component in Figure 1 - lower panel).

The Supplemental Materials note that:

Relationship between Papuan, Tianyuan and EA/SEA/Ancients

We find support for Australians and Bougainville islanders forming a clade with Papuans, to the exclusion of Tianyuan (Table S14). In turn, many EA and SEA form a clade with Tianyuan, to the exclusion of Papuan (Table S13). Onge, Jarawa and Jehai do not form a clade with either Papuans or Tianyuan (Table S13, S14), but have a stronger affinity to Papuans than to Tianyuan (Z = 3 - 4.2, for D(Onge/Jarawa/Jehai, Tianyuan; Papuan, Mbuti)).

Relationship between Onge, Tianyuan and SEA

We find Onge, Jarawa and Jehai form a clade with Onge to the exclusion of Tianyuan, but no other EA or SEA population form a clade with Onge, to the exclusion of Tianyuan (Table S17).

Relationship to Surui and Mixe

We tested for a specific affinity in the Surui to our ancient samples, as was previously detected in Papuans, Onge and Tianyuan. For the 2240k panel, we find that D-statistics of the form D(Mixe, Surui, Group 1 individual, Mbuti) are high but non-significant (Z = -2.18 and -2.5, using Ma911 and La368, as the Group 1 representative, respectively) (Table S19).

Relevant data is also contained in a paper looking at the genetics of modern Indonesia.

What cultural and technological and ecological impact did each of these waves have? Were there climate or other events that drove these transitions?

One plausible possibility in my mind is that the Tianyuan individual, the Onge, Mainland Southeast Asian Negritos, and pre-admixture Ancestral South Asians are all part of a wave of Asian migration after an initial pre-Papuan wave ca. 70,000 years ago, but at least somewhat before the Tianyuan individual ca. 40,000 years ago. In that scenario, these second wave hunter-gatherers may have been able to conquer pre-Papuan first wave hunter-gatherers by virtue of the fact that they had domesticated dogs at their disposal, while the pre-Papuans did not (or if they did, didn't bring them with them on their maritime colonization journey). Certainly, we know that the founding population of the Americas which would have arrived in Beringia more than 20,000 years ago had dogs (a conclusion that tends to trump estimates for dog domestication at just 15,000 years ago or less). I previously explored this hypothesis at greater length here as a way to help explain the dilution of Denisovan ancestry in mainland Southeast Asia and parts of Island Southeast Asia that were previously part of Sundaland.

This time frame is a fairly good fit the genetically and archaeologically estimated time frame in which dog were domesticated: One scholar has argued at book length that dog domestication was a key factor in the Upper Paleolithic revolution and also in giving modern humans an edge over the Neanderthals in Europe. See also here. There have even been some studies that located the domestication of the dog event (if there was just one primary one) in Southeast Asia, although there is not a consensus on that point.

It also isn't too far afield from estimates of wave of Asian migration in the Upper Paleolithic based upon analysis of the phylogeny of uniparental markers in modern populations in light of known mutation rates.

Archaic hominins in Southeast Asia

We know that archaic Homo erectus was present in Southeast Asia before any modern humans. We know that Homo floresiensis was present in Southeast Asia before any modern humans. We are quite confident that Homo floresiensis were not Denisovans because their physical anthropology is too archaic even relative to Homo erectus.

In the modest straightforward scenario by which Papuan/Australian folk receive Denisovan admixture, there were Denisovans in Southeast Asia before any modern humans.

We don't know with any great confidence which archaic hominins were present to have first contact with modern humans, although Denisovans must have been among them.

The paper has this to say about Denisovan admixture:

We find that the genetic diversity found in present day SEA populations derives from at least four prehistoric population movements by the Hoabinhians, an “Austroasiatic-like” population, the Austronesians and, finally, additional EA populations into MSEA. We further show that the ancient mainland Hoabinhians (Group 1) shared ancestry with present-day Onge of the Andaman Islands and the Jehai of peninsular Malaysia. These results, together with the absence of significant Denisovan ancestry in these populations, suggest that the Denisovan admixture observed in Papuans occurred after their ancestors split from the ancestors of the Onge, Jehai and the ancient Hoabinhians. This is also consistent with the presence of substantial Denisovan admixture in the Mamanwa from the Philippines, which are best modeled as resulting from an admixture between Austronesians and Papuans, not Onge.

I think a model in which Papuans comes first, and entirely separate wave of modern humans akin to the Onge arrive next is a better description of the most plausible inference, even though they may be technically equivalent.

Why don't researchers integrate more kinds of evidence?

I remain puzzled by the reluctance of investigators to more heavily integrate distinct evidence from the modern mix of human uniparental markers, modern autosomal DNA in humans, ancient and modern plant genetics, ancient DNA, linguistics, and archaeology into a single comprehensive analysis which would be so much more powerful. It isn't as if these are lone wolf investigators who can't play well with others. These papers are done by large teams with lots of well informed feet on the ground. Some of this may flow from the incentives to publish in the smallest publishable unit and to have relatively short papers in science relative to the humanities or law. But, one can get much more powerful conclusions by integrating all of the available evidence.

The paper does outline that "Two layer model" that its data eventually confirms:

[T]he Two Layer model advocates for two major dispersal waves into SEA, where EA farmers replaced the original Hoabinhian inhabitants across SEA through a major demographic southward expansion ca. 4 kya. The exception to this would be the isolated populations of the Andaman Islands, peninsular Thailand/Malaysia and the Philippines which are considered the primary descendants of Hoabinhian hunter-gatherers. Under this model, the migratory wave of farmers originated in present-day China, where rice and millet were fully domesticated in the Yangtze and Yellow River valleys between 9-5.5 kya, and paddy fields developed by 4.5 kya. Farming practices are thought to have accompanied these populations as they spread southward through two main routes – an inland wave associated with the expansion of Austroasiatic languages, and an island-hopping route associated with Austronesian languages which eventually reached the Pacific. Within mainland SEA (MSEA), exchanges with EA appear to have continued in the recent past, however, the extent to which these expansions had a genetic impact on the indigenous populations is unknown.

Some of this gap is filled in with efforts like Razib's excellent post on the topic which contextualizes this paper's findings in a larger cultural context and also ties it in to relevant aspects of South Asian pre-history like the origins of the Munda people of India. With respect to the two waves of migration after the "first farmers" ca. 4 kya, he explains:

The authors also detect migrations into Southeast Asia besides that of the Austro-Asiatics and Austronesians. One element seems correlated with the Tai migrations, and another with Sino-Tibetan peoples, most clearly represented in Southeast Asia by the Burmans. The excellent book, Strange Parallels: Volume 1, Integration on the Mainland: Southeast Asia in Global Context, c.800–1830, recounts the importance of the great migrations of the Tai people into Southeast Asia ~1000 A.D. Modern-day Thailand was once a flourishing center of Mon civilization, an Austro-Asiatic people related to the Khmers of Cambodia. The migrations out of the Tai highlands of southern China reshaped the ethnography of the central regions of mainland Southeast Asia. The Tai also attempted to take over the kingdoms of the Burmans. Though they failed in this, the Shan states of the highlands are the remnants of these attempts (tendrils of the Tai migrations made it to India, the Ahom people of Assam were Tai). Vietnam, shielded by the Annamese Cordillera, came through this period relatively intact. It is also well known that Cambodia’s persistence down to the present has much to do with the shielding it received from France in the 19th century in the wake of Thai expansion.

What Does This Mean For South Asian Pre-History?

With respect to the Munda of India, Razib notes that:

They detect shared drift between Austro-Asiatic people and tribal populations in northeast India. This is not surprising. A 2011 paper found that Munda speaking peoples, whose variant of Austro-Asiatic is very different from that of Southeast Asia, are predominant carriers of Y chromosome O2a. This is very rare in Indo-European speaking populations, and nearly absent in Dravidian speaking groups. Additionally, their genome-wide patterns indicate some East Asian admixture, albeit a minority, while they carry the derived variant of EDAR, which peaks in Northeast Asia. 

One debate in relation to the Munda people is whether they are primal and indigenous, or whether they are intrusive. The genetic data strongly point to the likelihood that they are intrusive. An earlier estimate of coalescence for O2a in South Asia suggested a deep history, but these dates have always been sensitive to assumptions, and more recent analysis of O2a diversity suggests that the locus is mainland Southeast Asia. 

Now that archaeology and ancient DNA confirm Austro-Asiatic intrusion into northern Vietnam ~4,000 years ago, I think it also sheds light on when these peoples arrived in India. That is, they arrived < 4,000 years ago. As widespread intensive agriculture came to Burma ~3,500 years ago, I think that makes it likely that Munda peoples arrived in South Asia around this period. 

I now believe it is likely that the presence of Austro-Asiatic, Dravidian, and Indo-Aryan languages in India proper was a feature of the period after ~4,000 years ago. None of the languages of the hunter-gatherer populations of the subcontinent remain, with the possible exception of isolates such as Nihali and Kusunda.

The recent origins of Austro-Asiatic, Indo-Aryan and Tibeto-Burmese languages in India are all established beyond what I would consider to be reasonable doubt through multiple lines of evidence.

The case of Dravidian, which is correlated, especially in lower caste populations, with Ancestral South Indian genetics that autochthonous to India and for whom the closest modern population is the Onge population of the Andaman Islands, is trickier, and one I've explored before. 

At a minimum, the close linguistic relations between the Dravidian languages suggest that this language family underwent a linguistic bottleneck, possibly sometime after the arrival of the Indo-Aryan invasion of India, from which all modern Dravidian languages derive, even if the pre-agricultural people of India spoke languages that were part of a family that includes proto-Dravidian.

It is also very plausible that the rise of the Dravidian languages, whether or not my bottleneck conjecture for the Dravidian languages is correct, is associated with the South Indian Neolithic revolution ca. 4500 years ago (i.e. around 2500 BCE), only a thousand years or less before the Indo-Aryan invasion. There is ample precedent of language replacement in favor of a dominant farmer language in association with the expansion of a newly food producing culture. 

This would be a few centuries older than Razib's casual estimate, but still reflects the same basic theme that the pre-agricultural hunter-gatherer languages of India are probably now entirely lost or are represented by only a couple of nearly moribund language isolates while untold scores or hundreds of other hunter-gatherer languages of pre-agricultural India (since hunter-gatherer civilizations appear to have had more linguistic diversity than early farmer civilizations in the fertile areas that first adopted farming) have been forever lost.

It is far less obvious, however, whether Dravidian's ultimate source (possibly a source prior to a bottleneck that impairs the usual linguistic methods of dating it) was home grown, becoming dominant while stamping out its neighbors, or if Dravidian has its source in the same population that brought the crops that made the South Indian Neolithic revolution possible as none of the core crops in that food production package are native to India. Some of those crops have origins in the Fertile Crescent and others arose in the wild and were domesticated in the African Sahel.

I've also explored potential genetic markers of an outside source for Dravidian, with Y-DNA T looking like a particularly promising marker in light of its geographical distribution within India, the fact that it is almost certainly invasive to India, and the fact that it was present in a place that would have been on the path of African Sahel crops to India, but I don't have data good enough to confirm or rule out those hypotheses definitively. Without more detailed sub-haplogroups of Dravidian Y-DNA T bearers, it is hard to date their antiquity, their diversity, and the place from which they made an invasive appearance in India. If it is a distinctly Indian and very basal clade of Y-DNA T, my hypothesis that it arrived with African Sahel crops is probably wrong. If it shows affinities in particular to clades of Y-DNA found in Yemen and Somalia and Ethiopia, and shows a star-like pattern of sub-haplotypes specific to India around 2500 BCE (per this paper by Dorian Fuller), it would strongly confirm my hypothesis.

The much anticipated ancient Harappan DNA evidence that should appear in published work any day now won't be much help because, as I have recent argued at length elsewhere, the Harappan language was unlikely to be a Dravidian language and while it may have shared some areal linguistic features with Dravidian, may not have even been in the same language family.