Resolutions in the Indian genetic layer cake

Gene ExpressionBy Razib KhanApr 24, 2011 5:54 AM


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Two years ago Reconstructing Indian Genetic History reframed how we should view South Asian historical genomics. In short, Indians can be viewed as a hybrid between a West Eurasian group, "Ancestral North Indians" (ANI) and a very different group, "Ancestral South Indians" (ASI), which had distant connections to West and East Eurasians. At least to a first approximation. Last fall I posted on a new paper which surveyed the Austro-Asiatic speaking peoples of India, and concluded that they were exogenous to the subcontinent. This is an interesting point. Prehistoric treatments of South Asia often use linguistic terms to denote putative ancient populations. One model is that first it was the Munda, the most ancient Austro-Asiatics. Then the Dravidians. And finally the Indo-Aryans.

These genetic data imply that the Munda arrived after the initial ANI-ASI synthesis.

The Munda people of India can be thought of as ANI-ASI, with an overlay of East Eurasian ancestry. Zack Ajmal's K = 11 ADMIXTURE run has highlighted some further issues. He has a set of Austro-Asiatic samples, as well as a host of Indo-Aryan and Dravidian speaking populations. I now believe we can now further clarify and refine our model of the peopling of India. Here it is: 1) ASI, circa ~10,000 years BP 2) ANI enters the subcontinent from the northwest, synthesis with ASI 3) The ancestors of the Munda enter from the northeast, synthesis with ANI + ASI in their region 4) A subsequent group of West Eurasians, related to the ANI, so I will term them ANI2, enters from the northwest and overlays the ANI + ASI synthesis. In the northeast quadrant of the subcontinent this group marginalizes the Munda people, who are either assimilated or escape to more remote locations. I believe that ANI2 is likely the Indo-Europeans, but it may be Dravidians as well 5) A second group of Austro-Asiatic peoples enters from the northeast, and synthesizes with the AN2 + ANI + ASI. In some regions they are absorbed (Assam), but in other regions they are culturally dominant (Meghalaya) Below are two plots which illustrate where I'm coming from. The "S Asian" component from K = 11 above seems to overlap, but is not identical to, ANI. The "Onge" component plays a similar role with ASI. The "SW Asian" and "European" elements are pretty straightforward. They're very closely related to the "S Asian" one, but they do separate from it. Their relationship to distant non-Indian groups as well as a gradient toward the northwest suggests to me a more recent arrival of this element.

Two patterns. For the Indo-European and Dravidian South Asian groups you see a vertical distribution which corresponds to populations which are a combination of ANI/ASI. But notice the perpendicular distribution of the Austro-Asiatic groups. The East Eurasian element to their ancestry means that they are not fully modeled by the two-way admixture. I believe that the the "Onge" fraction, which tracks ASI, is overestimating ASI in the Austro-Asiatic because the this proportion just seems way too high in many Southeast Asian and Dai groups to be plausible to me as a prefect proxy for ASI in them. But in any case, note that the Austro-Asiatic groups seem to be mostly a mix of ANI/ASI like other South Asians. There is clearly one outlier population. I'll get to them. Below is a plot which shows the ratio of the sum of AN2 over the stabilized hybrid proportion.

We know from Reconstructing Indian Genetic Historythat South Indian tribals and Dalits have a fair amount of West Eurasian ANI. But, from the genome bloggers, and especially Zack's further analyses, we can see that there is a further component of West Eurasian ancestry which is probably not ANI, but post-dates it. These components have affinities to Southwest Asia or Central Eurasia. They're labeled "SW Asian" and "European" in Zack's K = 11. Here's the big thing you notice: this element increases southeast-northwest, and low caste to high caste. It's almost absent among many Dravidian populations. It is very common in the northwest of the subcontinent. Again, except for that one outlier, the Austro-Asiatic groups almost totally lack AN2, just like some Dravidian tribals. On the other hand, even the most AN2 groups in South Asia clearly have some ASI and ANI. But having ASI and ANI does not guarantee AN2. The East Eurasian component found in the Austro-Asiatics seems constrained to the northeast of the subcontinent by and large. Finally, we have the outlier Austro-Asiatic group. These are the Khasi. They are are not Munda, and seem to have closer relationships to other East Eurasian populations. They also have a small, but noticeable AN2 component. What's going on? I believe that the Khasi arrived in northeast India after those who brought AN2 had already marginalized the Munda. Some of the Khasi were probably assimilated into the post-Munda (Indo-European or Dravidian speaking) peasantry. But some of the Khasi maintained their identity in the highlands, where they also intermarried with the post-Munda population, which had AN2. In contrast the Munda who retained their cultural identity had withdrawn and disengaged. Here's a table for you perusal (remember that ASI is inferred):

GroupLanguageStatusS AsianOngeE AsianSW AsianEuroSiberianASI

















North KannadiDravidian57%37%1%1%2%0%56%

SatnamiIndo-EuropeanL Caste49%36%8%1%3%0%56%


KamsaliDravidianL Caste59%35%1%2%0%0%54%

VysyaDravidianMid Caste62%34%0%2%0%0%53%



NaiduDravidianU Caste59%32%0%4%2%1%50%

LodiIndo-EuropeanL Caste58%32%1%2%6%0%50%

VelamaDravidianU Caste60%29%0%7%2%0%46%

SrivastavaIndo-EuropeanU Caste56%28%0%4%10%0%44%

Gujaratis aIndo-European64%26%0%3%6%0%42%


Cochin jewsDravidian50%24%1%16%7%0%39%

VaishIndo-EuropeanU Caste52%24%0%6%15%0%39%

Gujaratis bIndo-European56%22%0%7%13%0%36%


Bene Israel JewsIndo-European45%19%0%26%8%1%32%

Kashmiri panditIndo-EuropeanU Caste51%18%0%12%15%2%31%


Singapore malay5%17%73%1%1%0%30%










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