Razib Khan One-stop-shopping for all of my content

September 26, 2018

Vietnamese are not that much like the Cambodians

Filed under: Cambodia,Historical Population Genetics,Vietnam — Razib Khan @ 11:45 pm

A comment below suggested another book on Vietnamese history, which I am endeavoring to read in the near future. The comment also brought up issues relating to the ethnogenesis of the Vietnamese people, their relationship to the Yue (or lack thereof) and the Khmer, and also the Han Chinese.

Obviously, I can’t speak to the details of linguistics and area studies history. But I can say a bit about genetics because over the years I’ve assembled a reasonable data set of Asians, both public and private. The 1000 Genomes collected Vietnamese from Ho Chi Minh City in the south. I compared them to a variety of populations using ADMIXTURE with 5 populations.

Click to enlarge

You can click to enlarge, but I can tell you that the Vietnamese samples vary less than the Cambodian ones, and resemble Dai more than the other populations. The Dai were sampled from southern Yunnan, in China, and historically were much more common in southern China, before their assimilation into the Han (as well as the migration of others to Southeast Asia).

Curiously, I have four non-Chinese samples from Thailand, and they look to be more like the Cambodians. This aligns well with historical and other genetic evidence the Thai identity emerged from the assimilation of Tai migrants into the Austro-Asiatic (Mon and Khmer) substrate.

Aside from a few Vietnamese who seem Chinese, or a few who are likely Khmer or of related peoples, the Vietnamese do seem to have some Khmer ancestry. Or something like that.

Narrowing the populations, and using Indians as an outgroup, I wanted to test the Vietnamese against a few select populations. In the graph to the right you see that they are on the same branch as the Dai, and there is gene flow from the Dia into the Cambodians, and from the Cambodians into the Vietnamese. These results actually suggest that the Cambodians have had more gene flow in than the Vietnamese.

If you check the ADMIXTURE plot though you notice that there is a huge range of variation in the Cambodians in terms of their ancestry. The Mon kingdoms to the west of Cambodia fell to the Tai, but Cambodia itself did not. It probably absorbed a fair amount of Tai ancestry though, even if it retained its cultural distinctiveness and character.

A PCA shows that the Vietnamese are a distinct cluster. Different from both the Dai and South Chinese. Some of the samples in the 1000 Genomes are shifted toward the Cambodians and others toward the Chinese.

Finally, I ran a three population test. Here are some results of interest:

o3 pop1 pop2 f3 z
Cambodia Dai Indian -0.00175342 -25.8023
Cambodia French_Basque Dai -0.00192501 -22.1918
Cambodia Vietnamese Indian -0.00122671 -20.5523
Cambodia French_Basque Vietnamese -0.00136869 -17.6703
Cambodia Dai Papuan -0.0013018 -12.7299
Cambodia Han_S Indian -0.000790546 -10.365
Cambodia Vietnamese Papuan -0.000929681 -9.57058
Cambodia French_Basque Han_S -0.00087403 -9.24743
Cambodia Han_S Papuan -0.000476145 -4.05509
Dai Han_S Cambodia -0.000106184 -4.15877
Dai Cambodia She -0.000123515 -3.04445
Han_N French_Basque Han_S -0.000690947 -6.04291
Han_N Han_S Indian -0.000379328 -3.60634
Han_S Dai Han_N -0.000562373 -20.0654
Han_S Vietnamese Han_N -0.000425554 -15.6301
Han_S Filipino Han_N -0.000560061 -14.4192
Han_S Filipino Naxi -0.000529454 -10.9605
Han_S Malay Han_N -0.00038395 -10.3834
Han_S Dai Naxi -0.000316766 -9.36127
Han_S Filipino Yizu -0.000377863 -7.59642
Han_S Dai Yizu -0.000271844 -7.57112
Han_S Cambodia Han_N -0.000272892 -6.90769
Han_S Vietnamese Naxi -0.000211726 -6.09433
Han_S Vietnamese Yizu -0.000178654 -5.79285
Han_S Filipino Tujia -0.000175578 -4.66665
Han_S Thailand Han_N -0.000270477 -4.17533
Han_S Vietnamese Tujia -9.7422E-05 -3.79926
Han_S Tujia Dai -8.98028E-05 -3.0287
Han_S Tujia Malay -6.18931E-05 -1.67189
Han_S She Han_N -7.74747E-05 -1.41452
Han_S Filipino She -3.55034E-05 -0.888484
Vietnamese Han_S Cambodia -0.000646757 -34.4357
Vietnamese Han_S Malay -0.000420205 -22.545
Vietnamese Cambodia She -0.000615643 -17.2252
Vietnamese Tujia Cambodia -0.000553747 -15.6249
Vietnamese Malay She -0.000460983 -13.9445
Vietnamese Tujia Malay -0.000384676 -12.4208
Vietnamese Dai Indian -0.000494414 -12.4142
Vietnamese Cambodia Han_N -0.000494095 -12.2197
Vietnamese Miaozu Cambodia -0.000421982 -11.4913
Vietnamese Malay Han_N -0.000378602 -10.154
Vietnamese French_Basque Dai -0.000524036 -9.99871
Vietnamese Miaozu Malay -0.000280205 -8.27434
Vietnamese Dai Papuan -0.000339828 -5.83617
Vietnamese Han_S Indian -0.000210588 -4.70338
Vietnamese Dai Han_N -0.000122813 -4.42234
Vietnamese Malay Naxi -0.000152052 -3.8678
Vietnamese Han_S Thailand -0.000147552 -3.73211
Vietnamese Cambodia Yizu -0.000145687 -3.71074
Vietnamese Cambodia Naxi -0.000133426 -3.20226
Vietnamese Burm Dai -5.79109E-05 -3.12906
Vietnamese Dai Yizu -7.91838E-05 -3.00809

September 25, 2018

A clash of civilizations along the lower Mekong

Filed under: Cambodia,Mainland Southeast Asia,Southeast Asia,Vietnam — Razib Khan @ 12:16 am

The lower Mekong region is a fascinating zone from the perspective of human geography and ethnography. Divided between Cambodia and Vietnam, until the past few centuries it was, in fact, part of the broader Khmer world, and historically part of successive Cambodian polities. Vietnam, as we know it, emerged in the Red River valley far to the north 1,000 years ago as an independent, usually subordinate, state distinct from Imperial China. Heavily Sinicized culturally, the Vietnamese nevertheless retained their ethnic identity.

Vietnamese, like the language of the Cambodians, is Austro-Asiatic. In fact, the whole zone between South Asia and the modern day Vietnam, and south to maritime Southeast Asia, may have been Austro-Asiatic speaking ~4,000 years ago, as upland rice farmers migrated from the hills of southern China, and assimilated indigenous hunter-gatherers.

But the proto-Vietnamese language was eventually strongly shaped by Chinese influence. This includes the emergence of tonogenesis. Genetically, the Vietnamese are also quite distinct, being more shifted toward southern Han Chinese and ethnic Chinese minorities such as Dai. My personal assumption is that this is due to the repeated waves migration out of southern China over the past few thousand years, first by Yue ethnic minorities, and later by Han Chinese proper. Many of these individuals were culturally assimilated as Vietnamese, but they clearly left both their biological and cultural distinctiveness in what was originally an Austro-Asiatic population likely quite similar to the Khmer.

As I have posted elsewhere it is also clear to me that Cambodians have Indian ancestry. Because unlike Malaysia Cambodia has not had any recent migration of South Asians due to colonialism, the most parsimonious explanation is that the legends and myths of Indian migration during the Funan period are broadly correct. There is no other reason for fractions of R1a1a among Cambodian males north of 5%. Depending on how you estimate it, probably about ~10% of the ancestry of modern Cambodians is South Asian (the Indian fraction is easier to calculate because it is so different from the East Asian base).

This is present in a few Vietnamese (Kinh) samples I have seen, but it is at a lower frequency. The reason for this Indian ancestry is that southern Vietnam became Vietnamese only in the last 500 years, and more intensively only in the last 200 years. The Vietnamese with Indian ancestry are almost certainly people who are from the southern part of the country with Khmer, or Cham, heritage.

Viet Nam: A History from Earliest Times to the Present is divided into three broad periods. The first is the development of the Vietnamese people as a synthesis of external elements from the north, and the Austro-Asiatic “sons of the soil.” Roughly from the Trung sisters down to the emergence of an independent Vietnamese state in the decades before 1000 AD. This is a narrative of perseverance. Unlike the Yue people of Guangdong and Fujian (and parts further north), the Vietnamese maintained their ethnic identity through long periods of Chinese rule. Transformed and reshaped by the Chinese rule, they emerged from it inflecting Sinic cultural elements within their own traditions.

The second phase is one of conquest. To some extent to an American who is used to seeing the Vietnamese as being catspaws in 20th-century geopolitics, it is painful to read about the drive south of the Vietnamese, and their extermination and assimilation of the earlier peoples and polities. Though they did not use a word such as “Manifest Destiny,” with hindsight it was clear that the Vietnamese were going to push along the coast southward until someone stopped them by force. As it happened, the rise of Vietnam coincided with the decline of Cambodia.

In the 18th and early 19th centuries, Vietnam and Siam (what became Thailand) fought over Cambodia in a manner analogous to occurred with Poland in the same period. The Vietnamese rule of Cambodia, especially in the first half of the 19th century, was concurrent with a drive toward more punctilious Confucianization of Vietnamese society along with a drive to forcing Buddhism into the private domain. This Confucianization entailed reinforcement of patriarchal rules, as well as attention to matters of uniform dress. The Vietnamese monarchy was attempting to create a Confucian society ruled by virtuous bureaucrats, overseeing a populace aware of and cognizant of the proper civilized forms.

Though never as extreme as Korea, Vietnamese Confucianism during this period was probably more pervasive than it ever became in Japan (where formal Confucianism tended to be the purview of the samurai class during the Tokugawa age). As part and parcel of civilizing Cambodia, making it Vietnamese, the conquerors attempted to do with the Khmer what they had done to their own people. Diminish the role and prominence of institutional religion, in this case, Theravada Buddhism, and educate the populace so that they could begin to produce their own virtuous bureaucrats.

One of the most interesting and curious aspects of the Vietnamese rule of the Cambodians is that the comments by the ruler of Vietnam and his subordinates clearly show some deep lack of the understanding of the distinctive nature Khmer culture as opposed to Vietnamese, in particular, northern Vietnamese, culture. They complain that though the Khmer maintain outward forms of proper decorum, they seem not to internalize the forms in a manner that would indicate they are sincerely civilized. The Vietnamese ruler marvels that the Cambodians have 1,200 years of history, but lack precise dates on their origins, and have vague dynastic periods (this is, to be frank, a very Indian feature). Additionally, the Khmer seemed obstinately attached to their Theravada Buddhist religion. When they rebelled against their Vietnamese overlords with the aid of Siamese invaders they declared that they did so to defend the Three Jewels of Buddhism. As is common in China, Vietnamese Buddhist sects periodically rebelled. But these rebellions were sectarian. In Cambodia Buddhism was not a sect, to be a Cambodia was to be a Theravada Buddhist.

In frustration, the Vietnamese ruler declared that “moral suasion” simply does not work with the Khmers! Though his regime was brutal, he was ultimately a Confucian who assumed exhortation would win out in the end.

Though the Vietnamese were aware of the cultural differences between themselves and the Khmer, they were not prepared for the task of swallowing a whole civilization distinct from their own.

This brings to mind comments of Victor Liberman, a scholar of mainland Southeast Asia, that Vietnamese Sinic Confucian statecraft was qualitatively different from the “solar polities” to its west. In his book Strange Parallels Southeast Asia in a Global Context, he outlines what he believes to be the features of these societies which allowed them to emerge in the early modern period with nation-states in a manner recognizable to Europeans. Over most of Southeast Asia Indian high culture spread in the period before 1000 AD (in fact, it was dominant in the southern two-thirds of modern Vietnam before 1500 AD). This meant the emergence of relatively politically loose societies around the charismatic figure of a monarch whose legitimacy was fundamentally religious and metaphysical. Southeast Asian kings aspired to be cakravartin. The turners of the wheel of history.

In contrast through steps and starts the Vietnamese developed a society which was in many ways a miniature shadow of that of China to the north. Instead of a divinely sanctioned monarchy, Vietnam produced subordinate kings to the emperor of China or in some cases a ruler who declared he was an emperor himself.  Their rule was sanctioned not by gods or priests, but impersonal Heaven and its mandate.

Whereas other Southeast Asian monarchs had court brahmins, bhikkhus, and later in the Malayan world ulema, the Vietnamese monarchs often put away the Buddhist monks and priests and hid any religious devotion from public view. On the Chinese model, the Vietnamese drove religion away as a helpmate, and subordinated religious impulse as ancillary to state functions and transformed it primarily to something that was a matter of popular enthusiasm and private devotion. Like the Chinese, the Vietnamese polity aimed to recruit and produce a large and broad class of virtuous administrators, many drawn from the agricultural populace itself to main social order and proper state function.

Liberman observes that the Chinese model necessarily requires greater coordination, concentration, and mobilization. Additionally, there naturally develops a cultural chasm between the simple peasant, and the educated bureaucrat, in such a society. In contrast in solar polities, the king and high nobility may be distant from the people as symbols, but the vast mass of peasants and clerics interact and engage on a popular level. Religious truths and ideals often can propagate on a dimension closer to the masses than the culture of the Confucian literati. While efficient and constitutive mobilization of the resources of solar polities is low at any given time, mass enthusiasm may be easy to trigger in punctuated bursts of activity around charismatic figures and exigent circumstances.

September 20, 2018

Indic civilization came to Southeast Asia because Indian people came to Southeast Asia. Lots of them

Reading Indonesia: Peoples and Histories. I selected it because unlike many books it wasn’t incredibly skewed to the early modern and postcolonial period. The author makes the interesting point that the Islamicization of western Indonesia and the rise of the great Javanese Hindu kingdom of Majapahit occurred around the same time. This, in contrast to the skein of Indic civilization which had been layered over maritime Southeast Asia for hundreds of years before the medieval period, starting around 500 AD with polities such as that of Kalingga.

As is usual in these sorts of books, it is emphasized that Indian civilization spread through cultural diffusion (in contrast to the fact that though Chinese trade was evident and present early on, the cultural impact was minimal). Any migrations are dismissed as legends, with the possible exception of a few elite religious functionaries.

I now believe this is wrong. I’ve discussed this extensively in the past, but the Singapore Genome Variation Project (SGVP) data set along with more Southeast Asians allows me to illustrate rather clearly the issues. The short of it is that it is highly likely that substantial South Asian ancestry exists within Southeast Asia, and that that ancestry is not just a function of colonial contact (e.g., as certainly occurred in Malaysia).

Click to enlarge

Merging the various data sets together I got 172,000 SNPs. The initial PC plot shows that Southeast Asian populations exist on a cline to Indians (these are Tamils from the SGVP). The Burmese and Malays in particular have a wide distribution toward the Indians, indicate of a range of ancestry due to continuous admixture. I separated the SGVP Malays into two groups: Malay, and MalayMix. The MalayMix are those Malays who are more shifted toward the Indians, and like the Burmese show wide variance. The Mala proper as a more straightforward cluster. Shifted toward Indians more as a group.

Click to enlarge

Zooming in you see that Malays (not MalayMix) are not too different from Cambodians, but are slightly shifted toward Papuans. Filipino samples are similar, but further from Indians. Please note that Malaysia and the Philippines both are somewhat shifted toward the Papuans, and these are two nations where there are still extant Negrito populations (in contrast to Cambodia).

Groups like Lahu, Dai, Koreans, and the Dayak samples from Borneo I put in there partly because I assumed they would be less admixed with South Asians.

Click to enlarge

Running the samples in an admixture model with K = 5, the results are pretty clean even in unsupervised mode. Part of this is that I did do some outlier analysis and pruning ahead of time.

The Melanesian sample has admixture from something that is maximized in Filipinos and the Borneo samples. This is clearly Austronesian. Notice that the Melanesian samples don’t have any other Southeast Asian ancestry. This indicates that the cosmopolitan nature of some Austronesian groups in maritime Southeast Asia were due to later admixture. In particular, I accept the argument of Lipson et al. that there was an Austro-Asiatic substrate that was absorbed by incoming Austronesians.

Because I was very particular about sample selection, the Indians are nearly fixed for their modal ancestral component. Notice which groups don’t have the Indian ancestry in Southeast Asia: the Borneo samples. Additionally, the frequency in the Philippines may be due to European ancestry. Notice that in the Filipino samples the more diverse individuals tend to have more Indian ancestry, perhaps indicative of cosmopolitanism.

The Lahu and Dai do not have any the Indian modal ancestry, suggesting that this was not present when the Southeast Asians arrived.

The Cambodians have the Indian modal ancestry, as do many of the Malays. The MalayMix population has a lot, as expected. They are rather like the Burmese samples in that way. Some of the Malays don’t have Indian ancestry though. I think this may be due to the reality that the Malay population is actually cosmopolitan in origin, absorbing Indians, Chinese, and, Orang Asli groups. The latter of which may not have had Indian ancestry.

Click to enlarge

Next I ran some Treemix. Cambodians and MalayMix have affinity with Indians, as you’d expect. The Malay group gets gene flow from the Borneo population, and is positioned rather closer to Indians.

Here are some f3-statistics. At least those with z less than -2.

out p1 p2 f3 z
Burm Korea Indian -0.00371314 -40.1063
Burm Dai Indian -0.00368793 -36.4354
Burm Lahu Indian -0.00363462 -33.3115
Burm Borneo Indian -0.00297696 -30.3724
Burm Filipino Indian -0.00222445 -24.3581
Burm Korea Papuan -0.00243075 -19.9711
Burm Dai Papuan -0.00213815 -15.6106
Burm Malay Indian -0.00133932 -15.233
Burm Korea NAN_Melanesian -0.00158736 -12.6428
Burm Cambodia Indian -0.000991136 -10.9863
Burm Lahu Papuan -0.00185199 -10.8255
Burm Dai NAN_Melanesian -0.0011808 -8.7863
Burm Lahu NAN_Melanesian -0.00136834 -8.35811
Burm Korea MalayMix -0.000470731 -7.64052
Burm Borneo Papuan -0.00105531 -7.04586
Burm Korea Cambodia -0.000388278 -6.74484
Cambodia Dai Indian -0.00166543 -19.5634
Cambodia Borneo Indian -0.00135571 -16.9002
Cambodia Lahu Indian -0.00106449 -10.9303
Cambodia Dai Papuan -0.00128886 -9.86858
Cambodia Borneo Papuan -0.000607278 -4.5826
Cambodia Dai NAN_Melanesian -0.000449035 -3.69865
Cambodia Lahu Papuan -0.000455081 -2.64151
Filipino Borneo Papuan -0.000462553 -3.8874
Filipino Borneo NAN_Melanesian -0.000325208 -3.54648
Malay Filipino Cambodia -0.000763086 -32.6034
Malay Borneo Indian -0.0020853 -29.1425
Malay Borneo Cambodia -0.000613918 -26.5048
Malay Borneo Papuan -0.00223031 -20.037
Malay Dai Indian -0.00136434 -14.4879
Malay Borneo NAN_Melanesian -0.00131484 -14.4241
Malay Dai Papuan -0.00188121 -13.6787
Malay Filipino Indian -0.000850623 -12.4534
Malay Borneo Burm -0.000447661 -11.0181
Malay Dai NAN_Melanesian -0.00122082 -10.1649
Malay Lahu Indian -0.000658295 -6.56147
Malay Filipino Papuan -0.00061669 -6.52747
Malay Borneo MalayMix -0.000237474 -5.75298
Malay Lahu Papuan -0.000942326 -5.35136
Malay Lahu NAN_Melanesian -0.000755618 -5.0158
Malay Korea Papuan -0.000473046 -3.65977
Malay Dai MalayMix -8.93679E-05 -2.12082
MalayMix Borneo Indian -0.00469843 -45.6919
MalayMix Filipino Indian -0.00377864 -39.6124
MalayMix Dai Indian -0.00412557 -35.9643
MalayMix Malay Indian -0.0028506 -33.0568
MalayMix Lahu Indian -0.00345861 -28.1738
MalayMix Korea Indian -0.00281846 -23.528
MalayMix Borneo Papuan -0.00322593 -21.9346
MalayMix Cambodia Indian -0.00192058 -19.5189
MalayMix Dai Papuan -0.00302494 -19.2884
MalayMix Borneo NAN_Melanesian -0.00208153 -15.6894
MalayMix Dai NAN_Melanesian -0.00213561 -14.4382
MalayMix Filipino Papuan -0.0019272 -14.0354
MalayMix Korea Papuan -0.00198522 -12.4299
MalayMix Cambodia NAN_Melanesian -0.00114701 -11.2074
MalayMix Malay Papuan -0.00123309 -10.69
MalayMix Cambodia Papuan -0.00119651 -10.578
MalayMix Lahu Papuan -0.00212514 -10.5372
MalayMix Malay NAN_Melanesian -0.00100416 -9.70624
MalayMix Lahu NAN_Melanesian -0.0017095 -9.61884
MalayMix Korea NAN_Melanesian -0.00120984 -7.54544
MalayMix Filipino NAN_Melanesian -0.000920147 -6.96775
MalayMix Borneo Burm -0.000446434 -5.966
MalayMix Filipino Cambodia -0.000336794 -5.33937
MalayMix Filipino Burm -0.000279165 -4.31016
MalayMix Burm Malay -0.000236247 -4.15308

No big surprises.

I’m trying to get rolloff to work on one of the Reich lab datasets, but it isn’t working (says not enough snps, but the file has 350,000!). I need to establish the admixture date. Perhaps I’ll look to use fineStructure?

Note that this paper shows that of 125 male Cambodians, 9 of them carry R1a1a. This is unlikely to come from French, and Cambodia, unlike Malaysia, doesn’t have a colonial Indian community.

More to come….

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