Ancient Indian Genetics At ASHG

At ASHG next Monday Niraj Rai will be presenting this poster, Reconstructing the peopling of old world south Asia: From modern to ancient genomes.

South Asia was one of the first geographic regions to be peopled by modern humans after their African exodus. Today, the diverse ethnic groups of South Asia comprise an array of tribes, castes, and religious groups, who are largely endogamous and have hence developed complex, multi-layered genetic differentiation. From such a complex structure, several questions have stood out from the research of our group and others that are only beginning to be resolved using modern sequencing techniques and targeted sampling of populations and archaeological specimens. Here, for the first time we have used ancient genomics approach to understand the deep population ancestry of Indian Sub- continent. Despite the rich sources available of modern Indian populations, success from ancient DNA specimens in the subcontinent have been limited. We have successfully analysed several museum samples and fresh excavation from the different part of India which provides us a wonderful opportunity to be able to relate these modern populations genetically with those in the past and build complex models of population mixture and migration in India. Using ancient genomics data from the human remains who have lived about 4-5 thousand years before present in North West and South of India, we are trying to understand the population history of Iron age people and their genetic relation with the North West of Indians and Iranian Farmers. Furthermore, we are providing a solid Genetic evidence that substantiates archaeological and linguistic evidence for the origins of Dravidian languages and the language of the Indus valley people.

I’ll probably be trying to make sure I catch Rai at the poster. I’m most interested in the South Indian samples. If they date to more than 4,000 years before the present, it will be quite interesting.

Below the fold is my response to a comment on The Roots of Indo-Iranian cultural genesis. My response is in bold. JR’s responses to my original comment are in italics.

as you know there more than those 3 now. none of the harrapan era individuals exhibit evidence of noticeable steppe drift.

What I know, and this is second hand info, is that there are 15 more InPe samples found by the Reich team, and they have enormous variation in the AASI levels. There is also ydna and mtdna which is South Asian. But I know nothing about the ANE/WSHG levels of these populations.

It seems likely that ANE/WSHG gene flow occurred into South Asia before the arrival of steppe people.

by sampling one individual you are reconstructing the phylogeny of whole populations.

That is true but we now know that the Rakhigarhi sample is so low coverage that it is practically useless.

I’m talking about more than something like PSMC. You can tune your priors even on a little data. Assume you have a population you don’t know about. You have 100 markers from one individual. That individual maps onto African populations. It doesn’t guarantee everyone else will map in the same way, but it tunes your priors.

Similarly, all InPe samples so far lack steppe ancestry. The size of the sample is small, and the quality varies, but we are getting more confident, not less.

So we have to fall back on the InPe samples. The InPe that we know so far were definitely not a homogenous group as you know it well. The question was really whether these groups lacked steppe_mlba which modern Indians have. But the paper unfortunately failed to demonstrate this conclusively.

Final conclusions are going to come down to 

  1. large sample sizes

  2. good geographic representation

But we can make preliminary bets. It seems likely to me that the bulk of steppe_mlba arrived after 2000 BC to South Asia. Not definitive, but likely.

If you look into the Supplementary section on South Asians in the Narasimhan paper, they only use Swat_IA, Swat_H, Punjabi & Mala to represent the post Harappan South Asians. And in the various qpAdm models they generate (using 2 separate sets of outgroups), the combination with the highest p-value for both the Punjabi & the Mala involve older steppe groups beside the steppe_mlba. It is only the Swat samples that probably show steppe_mlba preference. But then again, the Swat samples show greater preference for steppe_mlba_west rather than steppe_mlba_east, which is again making no sense archaeologically.

So there are no clear answers. And to top it all, the authors implicitly assume in their qpAdm models that South Asians have to be modelled as comprising of 3 streams – steppe, Iran_N groups, AASI – to arrive at their conclusion.

the Loschbour ancient genome form luxembourg was the first mesolithic western european hunter-gatherer. *every subsequent mesolithic hunter-gatherer has been genetically very smilar*, across all of western europe. that’s because they went through a bottleneck and range expansion

But we do not know that such a range expansion took place among Harappans. And it appears that they are arguing Harappans being endogamous already and having population structure which goes against the idea of a range expansion.

This is not correct. When you undergo range expansion you will admix with the population beyond the frontier. This will produce dilution (or not, depending on population densities).

At any rate, the 2 scenarios are different, we are comparing a hunter gatherer society with a complex Bronze Age urbanised society. In Harappan times, if there was a range expansion, it was likely to be more among the less developed populations in Inner India or among the Harappans it is more likely to be restricted to the elites.

when i say *steppe* i’m talking specifically of the genetic element that is Yamnaya+EEF, which is the distinctive european back-migration into the steppe after the corded ware western migration. this component probably has added iranian farmer+ANE/WSHG in some fractions.

Though I was initially reluctant to accept this – it appears that the more steppe rich South Asian groups also have slightly more ANF/EEF. The Daamgard et al paper argued that these Northern groups also have CHG which is lacking in others. One may argue that this could only come from steppe_mlba. But then the Harappans were already interacting with Iranians, Central Asians and the Mesopotamians and probably the Caucasus groups as well. This could very well have brought in ANF and CHG in their genetic mix and we do not need to resort to a steppe_mlba explanation for it especially as the archaeological evidence is quite lacking.

otoh the incoming group could have been heterogeneous with non-steppe lineages ‘hitchhiking’. this seems to have occurred in europe: haplogroup I1 shows a star-phylogeny just like r1b and r1a. i’m pretty sure it was integrated into the indo-european expansion after cultural and biological assimilation.

Could be. Or it maybe that the reality of things were very different from how it is being interpreted.

perhaps r1a1a-z93 isn’t connected to indo-aryans necessarily, though it is sufficiently

I think that the Harappans, East Iranians and Central Asians were already IE. So even if R1a z93 expanded locally, considering how Poznick et al dated the South Asian z93 to between 2500 – 2000 BC, it is more likely, in my opinion, to be related to Indo-Aryan expansion. Nothing else that we know of historically can explain the widespread South Asian presence of this Bronze Age lineage.

But this would ofcourse mean that the steppe_mlba also received R1a Z93 from South Asia. At present state of our knowledge, there is no evidence so far to support such a claim unless we can show some sort of admixture in steppe_mlba from Harappans or BMAC or Shahr I Sokhta.

It is possible for Harappans to have been IE and not Indo-Aryan. I am skeptical of this scenario, but it’s not impossible. Indo-Aryan is clearly related to Indo-Iranian cultures which came out of the Eurasian steppe.

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15 thoughts on “Ancient Indian Genetics At ASHG”

  1. Thanks for this. What is nice to read is that they are talking about samples from multiple sites. I hope the presentation throws more light on this.

    I hope you come back with some fresh data. All the best

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  2. Curious about an earlier comment you made.

    “I don’t have the time or interest to read Guha’s India After Gandhi. Also, my friend Reihan Salam has indicated to me it’s a more tendentious work than most are willing to admit.”

    Why do you say so?

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    1. Why do you say so?

      i think reihan suggests it is a particular view from the indian national elite (center-left?). but indian americans take it to be the ‘last word’.

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      1. Guha et al may be called JNU elite aka national elite . They usually base their history or conclusions on western researchers in history, linguistics, etc. They have painted Hindutva views as loony at best , fascist at worst. Hindutva guys are also not terribly good at intellectual arguments and even their intellectuals like Arun Shourie have been pushed to the background.

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  3. Humans have been present in South India for 125000 or more

    https://www.nature.com/articles/nature25444

    https://www.firstpost.com/tech/news-analysis/ancient-stone-age-tools-found-in-tamil-nadu-suggest-reframing-of-out-of-africa-theories-4329961.html

    Actually , Attirambakkam near Madras International Airport , has been under archaeological investigation for 150 years. It is also called Paleolithic factory due to large quantity of tools found there The people in prehistoric period used to put the dead in earthen pots and bones can be preserved for a long time as long as it is not broken and dispersed. If they can search specifically for such remains , it will add to the genetic data.

    Just yesterday, I saw a program on the TV in which Mexico has been seen from the air with infrared and laser devices and that has turned up 50 times more Maya remains than what is known at present and the Maya population during 6th century has been estimated at 20 million.

    such aerial archaeology can yield a wealth of archaeological data and I am sure more thorough scanning from air well yield more paleolithic sites and with it human remains.

    Mega urbanization coupled with historical and archaeological insensitivity which has been going on for the last 20 years will destroy these remains forever.

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    1. Razib, feel free to cut my discussion off (I am flying intercontinent and jetlagged), but …

      All human and pre-human occupation in the subcontinent is temporally bisected by Toba. The thickness of volcanic ash on the continent wiped out any human or achaic hominim occupation 74,000 years ago; the subsequent 1,800 year ice age meant that no human survived this, and all population is out of Africa (or from Eurasia if you are strongly multi-origin). All of Atrrambakkam have not been established as human. Middle-paleolithic is not assuredly human. Ravi K. did establish Jwalapuram as human, but survivability is in question, and even then what mtDNA that is not from Africa do they represent?

      The only people with L3 (and their descendants of M, N) crossed over no earlier than 70K BP. I am afraid out of all of jwalapuram and Attrambakam, there may be no mt or Y left, even if they survived Toba, in spite of what Pettraglia says. Unlike in Anatolia or eastern Asia there is no evidence of neanderthal (OK, humanoid) introgression specific to India. All of this will be in the first few sections of a book of Indian genetics, if Reich (or Razib) publish one.

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      1. In two locations in TN, we have found hand axe and tools, one is Pallavaram near the airport. Atrambakkam is near lake Poondi and that is where r.B.foote found the tools in 1863. There has been almost continuous excavations in Atrambakkam since then, but the entire area is 12o’ X 1000′, and I do not anticipate anything more to be found. People can drive on the road from Thiruvalloor that is on the lake shore; I will get some pictures if anyone is interested when I get to chennai, in a few days. It is not a large excavation, a-la Turkey or Tanzania. Practically there is not much here.

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          1. I think there is some misunderstanding; they left Africa 70K years ago; but they did not arrive at Sahul much earlier than 50 K years; thus they became split from Eurasians about 50K years ago. IF, the AASI is considered part of this diaspora, then they also can be considered split from the Eurasian (50 K years), whereas the Iranian Farmer (the second component of ASI) split from Eurasian about 10K years ago (may be earlier). However, there is no evidence of mixing with any remnant with local hominids (like Denisovans) or humans in the subcontinent yet. This is attributed to Toba incident.

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  4. VijayVan, can you contribute an article about how humans lived in India 125 K years ago? What type of human? What type of DNA? What type of tools?

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      1. Oh, you were one step ahead of me. If non homo sapien hominids were technologically advanced, surely they would left many more proofs of their tech prowess than miserable stone tools. I don’t know why my post is stuck in moderation for many hours, the problem would not have come if non homo sapien hominids were moderators I guess.

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        1. VijayVan, less than one in a million materials last Akaala or father time. And even then we need to know where exactly to look. We also need to be open to civilizations, cultures and technologies different from our own.

          Inertia and post modernist academia is very resistant to accepting ancient civilizations that reject their post modernist ideology. Academics drag their feet. It is only now becoming mainstream to say that many ancient Egyptian sites existed during the last ice age (which ended 9700 BC) for example.

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  5. “Furthermore, we are providing a solid Genetic evidence that substantiates archaeological and linguistic evidence for the origins of Dravidian languages and the language of the Indus valley people.”

    Very interesting, “origins” of the dravidian language? Should I daresay they think there is a connection to the IVC people? Would love to see that presentation.

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