South Asian genetics, the penultimate chapter

A long post at my other blog, The Maturation Of The South Asian Genetic Landscape, a reflection on the important preprint The Genomic Formation of South and Central Asia. Shorter:

  1. The original inhabitants of the Indian subcontinent who descent from the “out of Africa” migration separated very quickly, ~50,000 years ago, from other eastern populations (East Asians, Andaman Islanders, Papuans, etc.). These are the “Ancient Ancestral South Indians” (AASI).
  2. Agriculturalists from what is today Iran seem to have entered and mixed with the AASI in the Indus Valley earlier than 5,000 years ago, and possibly as early as 9,000 years ago. The only samples they have are from extra-Indian sites, in Central Asia and eastern Iran, as outlier individuals. They call these “Indus_Periphery” (I call then InPe).
  3. The “Ancestral South Indians” (ASI) were created from a mixing of InPe with AASI still extant in much of South Asia ~4,000 years ago.
  4. Between ~4,000 and ~3,200 years ago populations from the steppe arrive, carrying admixture from Iranian farmers, as well as people from the steppe (Andronovo-Sintashta?). They mix with the ASI population, though a few groups, such as the Kalash, mix directly with InPe, and create unmixed “Ancestral North Indian” (ANI).
  5. Subsequent mixing between ASI and ANI populations in various fractions accounts for most of the variation in South Asia.
  6. Some groups are enriched for “steppe” as opposed to the Iranian agriculturalist that first came with InPe. In particular, Brahmins. The hypothesis then is differential ancestry of Indo-Aryan heritage persists to this day.
  7. The Munda of northeast India have a somewhat different origin, mixing Southeast Asian ancestry with ASI and further AASI. The fact that unmixed AASI were present in South Asia indicates that the Munda arrived before the full mixture was complete. Though Austro-Asiatic expansion into northern Vietnam dates to ~4,000 BC, so I think it can’t be that early.

Things I now think are unlikely:

  • Indo-Aryan interpenetration with non-Indo-Aryans in the IVC before 4,000 years ago (I was somewhat agnostic on this). The date for migration now seem very close to the “Classical Model” of arrival around 1500 BC.
  • The AASI is very diverged from the Onge, who form a clade with mainland Southeast Asian Negritos. I now think it is likely that the AASI were primal, and not migrants from Southeast Asia.

It would be nice if the results were published from the Rakhigarhi site, which dates to 4,600 years ago. But it seems less and less necessary. Perhaps at some point we’ll get enough samples from Pakistan to generate a reasonable model….

The Indian chapter of Who We Are and How We Got Here

Since Who We Are and How We Got Here is out I thought I would spoil the “India chapter” (though you should buy the book!).

– The “Ancestral North Indians” are best modeled as a 50/50 ratio of Yamna-type people from the steppes & “Iranian farmers.” The implication is that the Indo-Aryans mixed with agriculturalists in the BMC on the way into South Asia.

– The “Ancestral South Indians” have about ~25% “Iranian farmer”, along with the indigenous component more like the Andaman Islanders.

Bow before me Dasa!

David Reich clearly believes in a model of the ethnogenesis of South Asian populations detailed in A genetic chronology for the Indian Subcontinent points to heavily sex-biased dispersals. Also, I think I can now say in public when I had lunch with him he indicated that he thinks this is the most likely model. Also, the West Eurasian admixture into South Asian populations is “male-mediated.” R1a1a-z93 for the win!

He also believes there were several admixtures. He notes that his group’s 2013 paper, Genetic Evidence for Recent Population Mixture in India, reported two admixture events in North India, but one in South India. And the North Indian populations had the most recent event. This makes more sense if you consider that much of the admixture probably happened in the Northwest, as a mixed population spread across the subcontinent.

Reich contends that long tracts of ANI ancestry in some North Indians indicate that later people arrived from the first ANI wave. Also, several populations have an atypical Yamna-Iranian ratio in their ANI ancestry, being enriched for Yamna, and not so enriched for Iranian. These are all Brahmin groups.

Finally, he unmasks some of the backstories of difficulties collaborating with researchers in India, who have to be sensitive to cultural and political pressures. 2009’s Reconstructing Indian Population History was hailed in India as refuting the “Aryan invasion theory,” but the evidence was on the contrary, and I said so at the time.

In Who We Are and How We Got Here David Reich makes an explicit analogy between the Indian subcontinent and Europe. Both protrusions from Eurasia are characterized by a synthesis of indigenous hunter-gatherers, intrusive pastoralists from the Eurasian steppe, and migrating West Asian farmers.

Notes on South Asian genetics, 2018

A “pure” Tamil Brahmin, Chandrasekhar

In the post below Zach observes that the progressive author of a piece criticizing Ajit Pai has to note she too is a Gaud Saraswat Brahmin. Of course, she is progressive and opposes casteism no doubt. But to me “caste-dropping” that you are a Brahmin is like criticizing standardized testing, while observing that you also aced your standardized test. Not that that matters. Or that it proves anything.

But I’m posting this because there was a section on the genetic purity of Gaud Saraswat Brahmin’s of Karnataka. It caught my attention because I knew it was likely false. I’ve looked at South Indian Brahmins, and they generally look like they have gene flow from other South Indians. Also, if you use something called your eyes you can see that some South Indian Brahmins do not look like pure Indo-Aryan specimens at all.

Several years ago my friend Zack collected a bunch of data via his Harappa project. We’ve come further since then, but it’s still one of the best sources of information we have. Looking at the data there, and elsewhere, we can say a few things about South Asian genetics.

  • Jatts are different. I don’t know much about Jatts personally, aside from the fact that they are quite proud of being Jatt online. But in Zack’s data, and my own analysis in the SAGP, Jatts are highly inflated for “European-like” ancestry compared to populations around them. They have the highest proportions in their part of South Asia. Even higher than Pathans.

If you asked me to say why, at this I do think Jatts do have a more recent gene flow than other groups in South Asia. If you talk to Jatts online about their history, you will know what their hypothesis for this exotic element is.

  • Brahmins are different from other South Asians, and from each other. It will surprise no one that Brahmins are often somewhat different from non-Brahmins genetically. But, they also differ from each other.

Both South Indian and Bengali Brahmins mixed with the local population. Probably on the order of ~25% of the ancestry of these two Brahmin communities can be attributed to the local substrate. But, if you correct for East Asian admixture Bengali Brahmins are actually quite similar to the Brahmins of the Gangetic plains to the west. This comports with history.

A similar fraction seems reasonable for South Indian Brahmins, though perhaps more. The key issue that I have in this case is that the “European-like” proportion of South Indian Brahmins is about half of that of North Indian Brahmins. This would indicate half dilution. The admixture was probably from the higher end of the non-Brahmin caste hierarchy.

To get a sense of what I’m talking about, here are some percentages:

Ethnicity Dataset N SIndian Baloch Caucasian NEEuro NEEuro ratio
ap-brahmin xing 25 49% 36% 3% 6% 6%
iyengar-brahmin harappa 8 47% 37% 4% 6% 6%
iyer-brahmin harappa 11 47% 37% 5% 5% 5%
brahmin-tamil-nadu metspalu 2 47% 38% 6% 5% 5%
tn-brahmin xing 14 47% 38% 6% 4% 5%
karnataka-brahmin harappa 5 46% 35% 5% 6% 7%
oriya-brahmin harappa 2 45% 35% 2% 8% 9%
kerala-brahmin harappa 1 43% 39% 4% 6% 6%
brahmin-uttar-pradesh metspalu 8 42% 36% 5% 12% 12%
bengali-brahmin harappa 8 41% 33% 5% 10% 11%
up-brahmin harappa 4 39% 37% 7% 11% 12%
bihari-brahmin harappa 1 39% 38% 5% 11% 12%
rajasthani-brahmin harappa 2 34% 36% 8% 12% 13%
punjabi-brahmin harappa 3 34% 39% 10% 11% 11%
kashmiri harappa 3 30% 37% 14% 9% 10%
pashtun harappa 7 19% 34% 20% 11% 13%
maharashtrian harappa 6 46% 35% 5% 5% 6%
tamil-nadar harappa 5 57% 31% 2% 0% 0%
gujarati-patel harappa 2 55% 41% 0% 0% 0%
bengali harappa 11 47% 27% 2% 4% 5%
ap-reddy harappa 6 54% 36% 3% 0% 0%

Don’t take the percentages as literal populations.

  • Some groups that think they are special are not so special. Kashmiri Pandits, for example, fancy themselves as somewhat better than other South Asians, often because of their West Asian or even European physical appearance. But the genetic data indicates ancestrally they’re not surprising in any way in the context of their geographic locale.
  • Geography is not that predictive. Well, it sort of is. But you see that groups like Chamars in Uttar Pradesh are similar to South Indian populations.