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.

2+