Rakhigarhi – Gene Expression

We’ve been waiting for two years now, and it looks like they’re about to pull the trigger, Indus Valley People Did Not Have Genetic Contribution From The Steppes: Head Of Ancient DNA Lab Testing Rakhigarhi Samples:

Niraj Rai, the head of the Ancient DNA Laboratory at Lucknow’s Birbal Sahni Institute of Palaeosciences (BSIP), where the DNA samples from the Harappan site of Rakhigarhi in Haryana are being analysed, has revealed that a forthcoming paper on the work will show that there is no steppe contribution to the DNA of the Harappan people….
“It will show that there is no steppe contribution to the Indus Valley DNA,” Rai said. “The Indus Valley people were indigenous, but in the sense that their DNA had contributions from near eastern Iranian farmers mixed with the Indian hunter-gatherer DNA, that is still reflected in the DNA of the people of the Andaman islands.” He added that the paper based on the examination of the Rakhigarhi samples would soon be published on bioRxiv (pronounced “bio-archive”), a preprint repository of papers in the life sciences.

At this point none of this is surprising. I also wonder if this preprint was hastened by the release of The Genomic Formation of South and Central Asia. It seems that the results here are totally consonant with what came before. My expectation is that the lone sample that they got genetic material out of will be similar to the “Indus Periphery” (InPe) individuals in the earlier preprint: a mix of West Asian with ancestry strongly shifted toward eastern Iran, and indigenous South Asian “hunter-gatherer.” That’s pretty much what Niraj Rai states in the piece. I think genetically the individual won’t be that different from the Chamars of modern day Punjab.

In fact, Rai, the lead researcher, ends by twisting the knife:

In other words, the preprint observes that the migration from the steppes to South Asia was the source of the Indo-European languages in the subcontinent. Commenting on this, Rai said, “any model of migration of Indo-Europeans from South Asia simply cannot fit the data that is now available.”

A major caveat here is that we’re talking about one sample from the eastern edge of the Indus Valley Civilization (IVC). I’m not sure that this should adjust our probabilities that much. From all the other things we know, as well as copious ancient DNA from Central Asia, our probability for the model which the Rakhigarhi result aligns with should already be quite high.

Again, since it’s one sample, we need to be cautious…but I bet once we have more samples from the IVC the Rakhigarhi individual will probably be enriched for AASI relative to other samples from the IVC. The InPe samples in The Genomic Formation of South and Central Asia exhibited some variation, and it’s likely that the IVC region was genetically heterogeneous.

But, this is going to be a DNA sample from an individual who lived 4,600 years ago within the orbit of the IVC when it was in its mature phase. That’s still a big deal. As most of you know the IVC is prehistory because we haven’t deciphered the seals which are associated with this civilization. But, the IVC clearly had relationships with West Asia and Central Asia, with parts of eastern Iran and the BMAC culture both being influenced and interaction with it. Traders who were likely from the IVC seem to be mentioned in Mesopotamian records.

Additionally, the genetics of one individual can be highly informative if it’s high-quality whole-genome data (I’m skeptical of that in this case). One could possibly even identify the time period that admixture between West Asian and AASI components occurred from a single genome, by looking at ancestry tract lengths.

A single sample isn’t going to falsify the idea held by some that steppe peoples were long present within the IVC. Perhaps they’ll show up in other samples? That’s possible, and it’s what I would argue if I held their position, but I think the constellation of evidence on the balance now does suggest that a relatively late incursion into South Asia is likely. The steppe ancestry with Northern European affinities shows up in BMAC only around 4,000 years ago. It is hard to imagine it was in South Asia before it was in Central Asia.

As I’ve been saying for a while it seems that though there will be more genetic work written on India in the near future, the real analysis is going to have to come out of archaeology and mythology.

It’s pretty clear that in Northern Europe the arrival of the Corded Ware peoples from the steppe zone resulted in great tumult. A linguistic analysis suggests that the languages of Northern Europe have words related to agriculture with a non-Indo-European origin, of common provenance. But we don’t have much in the way of mythos about the arrival of the Corded Ware.

In contrast, India has a rich mythos which seems to date to the early period of the arrival of the Indo-Aryans. One interpretation has been that since these myths seem to take as a given that Indo-Aryans were autochtonous to India, they were. But the genetic data seem to be strongly suggesting that the arrival of pastoralists occurred in South Asia concomitant with their arrival in West Asia, and somewhat after their expansion westward into Europe. Indian tradition and mythos could actually be a window into the general process of how these pastoralists dealt with native peoples and an illustration of the sort of cultural synthesis that often occurred.

Tony Joseph has an interesting piece up, Who built the Indus Valley civilisation?, which people are asking me about via email. First, I don’t have any inside information. Last I heard in September was that the Rakhigarhi results were “one or two months away,” like they have been for a year or so. So I put it out of mind.

In any case, here are the important points:

All this could now change thanks to the science of genetics and four ancient skeletons excavated from a village called Rakhigarhi in Haryana. The four people to whom these bones once belonged — a couple, a boy and a man — lived roughly 4,600 years ago when the Indus Valley civilisation was in full bloom.
…
In the three-and-a-half years since its excavation, Shinde has brought together scientists from Indian and international institutions like the Centre for Cellular and Molecular Biology, Hyderabad (CCMB), Harvard Medical School, Seoul National University, and the University of Cambridge to work on different parts of the project, including extracting and analysing DNA from these ancient people, reconstructing their faces, and studying the remains of their habitation to understand their daily habits and ways of life.
The DNA analysis will also help figure out their height, body features, and even the colour of their eyes….

Joseph also asserts that the publication will happen in a “leading international journal” in a month or so. If I had to bet, I’d say Nature.

Harvard Medical School suggests to me they finally got David Reich’s group involved. ~~As for Cambridge University, Eske Willerslev now has an appointment there. He’s apparently assembling a paleogenetics group.~~

The piece specifically highlights Y and mtDNA. But if they are talking about height, body features, and color of eyes, they must have gotten genome-wide data. ~~If Eske Willerslev is involved they may have sequenced the whole genome at some coverage of at least one of the samples.~~

If I had to bet I think the Rakhigarhi samples will be Y haplogroups J2 or the Indian branch of L, and the mtDNA will be an Indian branch of M. In terms of genome-wide patterns they will exhibit a mixture between West Eurasian ancestry, with strong affinities to Near Eastern farmers from the Zagros, and what we now term “Ancestral South Indians” (AS), who descend from the aboriginal peoples of the subcontinent, and are genetically somewhat closer to East Eurasians than West Eurasians (to be fair, I think it is not implausible that much of ASI heritage is the product of westward migration out of Southeast Asia during the Pleistocene and early Holocene).

Overall, genetically these samples may look the most like South Indian non-Brahmin middle-to-upper castes. Think the Reddy people of Andhra Pradesh. Additionally, going back to R1a1a-Z93, I do think it was intrusive with the Indo-Aryans. Its highest frequencies do tend to be among upper castes, and there is an increasing cline toward the northwest of the subcontinent.

ButR1a1a-Z93’s presence at appreciable frequencies in South India among non- Brahmins, including tribal populations, indicates a more complex ethnogenesis of Dravidian speaking groups than we might have realized. Priya Moorjani told me specifically that 4,000 years ago there were “unmixed ANI and ASI groups” in the subcontinent. I think for the former she’s picking up the signal of intrusive Indo-Aryans. But what about the latter? I doubt there were unmixed ASI in the Indus Valley. But they probably still persisted to the south and east when the Indus Valley people were in decline and the Indo-Aryans arrived. The South Indian Neolithic dates from 3000 to 1400 BC.

Here my moderate confidence sketch. The collapse of the Indus Valley civilization was probably ultimately due to the fact that these early antique societies were not very robust to exogenous shocks and endogenous decay of asabiya. Once these societies, which have accumulated some level of surplus wealth by squeezing it out of the Malthusian margin, start to totter social collapse and dissolution can happen fast, and barbarian groups outside of the gates with more social cohesion can engage in a takeover.

In the case of the collapse of the Sumerian-Akkadian civilization, the barbarian Amorites actually took over and maintained cultural continuity. In post-Roman Britain, the Roman civilization collapsed in totality, and “Roman Christianity” had to be reintroduced from the European continent and from the Celts into Anglo-Saxon England. The barbarian takeover resulted in the total cultural obliteration of the Britons. Finally, you have instances such as post-Roman Gaul, which transformed into Francia. Unlike the case of the transition from the rule of the Third Dynasty of Ur to that of the Amorites, the Frankish rulers oversaw a wholesale reimagining of the identity of the people of Gaul. Even as late as 800, a ruler such as Charlemagne still spoke a dialect of German as his first language. And yet the Franks of Neustria were ultimately transformed and became one with the “Romans” whom they ruled.

In the post-Harappan world of northwest India I suspect something close to the Anglo-Saxon precedent is likely. Though the majority of the ancestry of the Upper Gangetic plain is not Indo-Aryan, a substantial proportion is. And this ancestry is detectable at lower fractions even among non-Brahmin Bengalis. In Central and South India the situation was probably more like Mesopotamia around ~2000 BC or Gaul post-500 AD. There were various sorts of interactions between Indo-Aryans and local populations, as well as the final assimilation of aboriginal peoples into Indo-Aryan and Dravidian speaking peoples.*

* The Munda people clearly have some East Asian ancestry. And, they are mostly a mix of ANI and ASI. But whenever I look at their genome-wide results it strikes me they may not have any Indo-Aryan ancestry. This may ultimately be totally comprehensible in light of the chronology of migration and segregation.

Update: One of the researchers involved indicates Eske Willerslev is not involved.