Indian ancestry in Southeast Asia is older than statistical genetic tests suggest
Posted on December 29, 2020 by Razib Khan

The panels above are from a new preprint, Reconstructing the human genetic history of mainland Southeast Asia: insights from genome-wide data from Thailand and Laos. It’s an OK preprint, marked mostly by the inclusion of a lot of samples from Thailand. The “southern Thai” samples are from peninsular Thailand, and there are Malays in there. The “central Thai” samples are from in and around Bangkok. The Mon seems to be sampled from Thailand as well.

Most of the papers on mainland Southeast Asian genetics are hard to follow because there isn’t a clear relationship in many cases between language and genetics, and linguistic classification can be dodgy. E.g., is Vietnamese Austro-Asiatic? The biggest difference is the old “Australo-Melanesian” substrate, and the ancestry brought by the farmers from the north. But these farmers themselves come out of a southern Chinese milieu where there isn’t a distinction. The biggest difference between a lot of the “Austro-Asiatic” and “Tai-Kadai” groups is how much Australo-Melanesian (Hoabinhian) ancestry they carry (the former carry more since they arrived earlier).

But the question of “Indian ancestry” is more interesting and a bit clearer. It seems obvious that a lot of Southeast Asian groups have South Asian ancestry. For twenty years it’s been clear that the HGDP Cambodian has a West Eurasian affinity, and many of us assumed it was simple “Ancestral South Indian” (ASI) shared lineage. Basically, the people from India to the South China sea were part of a genetic continuum before the intrusion of West Asians into South Asia and Northeast Asians into Southeast Asia. But this is wrong. The Indian ancestry clearly exhibits “Ancestral North Indian” heritage. In Cambodia itself on the order of 5% of the men seem to carry Y haplogroup R1a1a. This is steppe-associated.

So the question is when did this come into the region? The preprint’s figure is a little misleading, though in the text it’s clearer: the statistics indicate a major admixture ~750 years ago. The Mon in particular have lots of Indian ancestry. 20% is probably a low bound figure for this group. When I ran ALDER I got about 750 years for Cambodia. There is zero chance that there was a large scale migration of Indians into Cambodia at that date. Unlike proto-Burma, Cambodia is also pretty far from mainland India.

The most plausible explanation is that these admixture dates are picking up the mixing between a Southeast Asian set of populations without much Indian ancestry, and a group of Austro-Asiatic people who had a lot of Indian ancestry from an earlier admixture.
https://www.gnxp.com/WordPress/2020/12/ ... s-suggest/