Indian ancestry in Cambodia was present ~2,000 years ago

Posted on January 5, 2020January 5, 2020 by Razib Khan

When STRUCTURE-style bar plots first emerged using the HGDP Cambodian samples, there were often strange residual components with affinities to South Asians. When Treemix was developed there were strange edges between South Asians and Cambodians. In discussions with Joe Pickrell, the author of Treemix, we both adduced this must be due to deep affinities to “Ancestral South Indians” (ASI). Though Cambodia had “Indic” cultural affinities, the standard model is that this was due to cultural diffusion, not gene flow. Then Spencer Wells told me that The Genographic Project had detected that many Cambodian males seem to carry the R1a1a lineage. Looking at the literature, several Southeast Asian groups carry West/South Eurasian haplogroups which are likey Indian-mediated (R1a, R2, and J2, to name three). The enrichment is notable in groups like the Thai and Khmer which are located at some distance from South Asia.

Out of curiosity, I decided to look at the “Cambodian Iron Age” sample from a recent ancient DNA paper. This sample dates to 100 to 300 A.D., the period of ancient Funan, which we know mostly though not exclusively through Chinese sources:

According to modern scholars drawing primarily on Chinese literary sources, a foreigner named “Huntian” [pinyin: Hùntián] established the Kingdom of Funan around the 1st century CE in the Mekong Delta of southern Vietnam. Archeological evidence shows that extensive human settlement in the region may go back as far as the 4th century BCE. Though treated by Chinese historians as a single unified empire, according to some modern scholars Funan may have been a collection of city-states that sometimes warred with one another and at other times constituted a political unity.

Look at the Iron Age sample it does seem it is notably “Indian-shifted” even compared to modern Cambodians. This could just be an artifact of ancient DNA, but when I looked at a few dozen ancient Vietnamese samples, only one exhibited this same pattern of being Indian-shifted. Reducing the dataset to the 55,000 SNPs that came back on this ancient sample, you see the result above (many of the modern samples don’t have the full complement of these SNPs).

Something on the order of ~5-10% of the ancestry of many Southeast Asian groups seems to be of Indian origin. Looking at the Malays in the Singapore Genome Project, some of them have clear recent Indian ancestry, but even removing all of those you see notable Indian-shift, just as you see with the Cambodians. In contrast, Vietnamese and Dayaks from Borneo don’t show any evidence of such admixture. Neither do samples from the Phillippines.

The question is when this admixture occurred then. A large number of Indians migrated to Southeast Asia during the colonial period to Malaysia and Burma. But some preliminary analysis suggests to me that this doesn’t account for all of the Indian ancestry there. And, it can’t account for Cambodia and Thailand at all (though there aren’t too many genome-wide samples from Thais, the Y chromosomes show the same pattern as the Khmer).

Over time the genetic data is going to coalesce and converge on the details, though I think we see where it’s pointing. At that point, it’s up to archaeologists and historians to make sense of it. This includes scholars of South as well as Southeast Asia. The genetic imprint of South Asians in Iran and Central Asia is rather modest compared to what one sees in Southeast Asia, so it’s an interesting contrast as to why.

Likely male-mediated Indianization in Southeast Asia

Posted on October 6, 2018October 6, 2018 by Razib Khan

Pop	N	R1a1
Cambodian	125	7%
Balinese	551	2%
Southern Han	166	0%
Northern Han	65	0%
Miao	25	0%
Hui	25	17%
Sala	43	21%
Bo’an	44	25%
Dongxiang	47	32%

Black, Michael L., et al. “Genetic ancestries in northwest Cambodia.”

In the comments below a reader has pointed out that there are Y and mtDNA results for Cham people.

This Austronesian group was once dominant in what was termed Annam by the French, the central regions of coastal Vietnam between the deltas flanking the northern and south (dominated by the Vietnamese and Khmer respectively). The Cham were a seafaring population and had extensive contacts with maritime Southeast Asian and the network of Austronesian peoples.

As such, the Cham were influenced by the currents of cultural change to their south, and as by the early modern era many had become Muslims. But a minority resident in Vietnam retained their Hindu religious identity, and this reflects a deep current of Indianization which took root among them in the centuries before 1000 AD. The boundary between ancient Champa and Đại Việt was also a civilizational boundary, between the elite culture of India and China.

The commenter states:

As far as I can see, this sample of Chams from Binh Thuan Province, Vietnam does not exhibit any clear South Asian influence in its mtDNA. This contrasts starkly with the significant (18.6% to 32.2%) South Asian influence that is apparent in the Y-DNA of the male subset of the same sample

This seems right. As you can see above I’ve found plenty of evident that R1a1a is found in Southeast Asia where it shouldn’t be. Notice that among northern groups in China R1a1a is pretty frequent too. Obviously from a different source, but the same general pattern. And in that case we have plenty of historical evidence of interaction with Indo-Europeans on the steppe.

I’m not very conversant in mtDNA. This paper argues that the Mon people of Thailand have some mtDNA affinities with India. I created this pivot table for readers to double-check (the “MO” populations are Mon).

The history of Southeast Asia, or perhaps more accurately the quasi-history of Southeast Asia since so many of the records are from China and elsewhere, indicates strong Indian influence in the period before 1000 AD. The standard model is that this is cultural diffusion. And by and large Southeast Asian peoples are are mostly indigenous. But, a non-trivial minority of their ancestry is recent, but pre-colonial, gene flow from the Indian subcontinent. Additionally, the imprint is easier to see in the Y chromosome than the mtDNA. The legends of marriages between Indian Brahmins and native princesses in places like Cambodia probably do reflect something real in the dynamics of the early Indianization.

A clash of civilizations along the lower Mekong

Posted on September 25, 2018September 30, 2018 by Razib Khan

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).