Indian genetics, the never-ending argument

I am at this point somewhat fatigued by Indian population genetics. The real results are going to be ancient DNA, and I’m waiting on that. But people keep asking me about an article in Swarajya, Genetics Might Be Settling The Aryan Migration Debate, But Not How Left-Liberals Believe.

First, the article attacks me as being racist. This is not true. The reality is that the people who attack me on the Left would probably attack magazines like Swarajya as highly “problematic” and “Islamophobic.” They would label Hindu nationalism as a Nazi derivative ideology. People should be careful the sort of allies they make, if you dance with snakes they will bite you in the end. Much of the media lies about me, and the Left constantly attacks me. I’m OK with that because I do believe that the day will come with all the ledgers will be balanced. The Far Left is an enemy of civilization of all stripes. I welcome being labeled an enemy of barbarians. My small readership, which is of diverse ideologies and professions, is aware of who I am and what I am, and that is sufficient. Either truth or power will be the ultimate arbiter of justice.

With that out of the way, there this one thing about the piece that I think is important to highlight:

To my surprise, it turned out that that Joseph had contacted Chaubey and sought his opinion for his article. Chaubey further told me he was shocked by the drift of the article that appeared eventually, and was extremely disappointed at the spin Joseph had placed on his work, and that his opinions seemed to have been selectively omitted by Joseph – a fact he let Joseph know immediately after the article was published, but to no avail.

Indeed, this itself would suggest there are very eminent geneticists who do not regard it as settled that the R1a may have entered the subcontinent from outside. Chaubey himself is one such, and is not very pleased that Joseph has not accurately presented the divergent views of scholars on the question, choosing, instead to present it as done and dusted.

I do wish Tony Joseph had quoted Gyaneshwer Chaubey’s response, and I’d like to know his opinions. Science benefits from skepticism. Unfortunately though the equivocation of science is not optimal for journalism, so oftentimes things are presented in a more stark and clear manner than perhaps is warranted. I’ve been in this position myself, when journalists are just looking for a quote that aligns with their own views. It’s frustrating.

There are many aspects of the Swarajya piece I could point out as somewhat weak. For example:

The genetic data at present resolution shows that the R1a branch present in India is a cousin clade of branches present in Europe, Central Asia, Middle East and the Caucasus; it had a common ancestry with these regions which is more than 6000 years old, but to argue that the Indian R1a branch has resulted from a migration from Central Asia, it should be derived from the Central Asian branch, which is not the case, as Chaubey pointed out.

The Srubna culture, the Scythians, and the people of the Altai today, all bear the “Indian” branch of R1a. First, these substantially post-date 6000 years ago. I think that that is likely due to the fact that South Asian R1a1a-Z93 and that of the Sbruna descend from a common ancestor. But in any case, the nature of the phylogeny of Z93 indicates rapid expansion and very little phylogenetic distance between the branches. Something happened 4-5,000 years ago. One could imagine simultaneous expansions in India and Central Asia/Eastern Europe. Or, one could imagine an expansion from a common ancestor around that time. The latter seems more parsimonious.

Additionally, while South Asians share ancestry with people in West Asia and Eastern Europe, these groups do not have distinctive South Asian (Ancestral South Indian) ancestry. This should weight out probabilities as to the direction of migration.

Second, I read some of the papers linked to in the article, such as Shared and Unique Components of Human Population Structure and Genome-Wide Signals of Positive Selection in South Asia and Y-chromosomal sequences of diverse Indian populations and the ancestry of the Andamanese. The first paper has good data, but I’ve always been confused by the interpretations. For example:

A few studies on mtDNA and Y-chromosome variation have interpreted their results in favor of the hypothesis,70–72 whereas others have found no genetic evidence to support it.3,6,73,74 However, any nonmarginal migration from Central Asia to South Asia should have also introduced readily apparent signals of East Asian ancestry into India (see Figure 2B). Because this ancestry component is absent from the region, we have to conclude that if such a dispersal event nevertheless took place, it occurred before the East Asian ancestry component reached Central Asia. The demographic history of Central Asia is, however, complex, and although it has been shown that demic diffusion coupled with influx of Turkic speakers during historical times has shaped the genetic makeup of Uzbeks75 (see also the double share of k7 yellow component in Uzbeks as compared to Turkmens and Tajiks in Figure 2B), it is not clear what was the extent of East Asian ancestry in Central Asian populations prior to these events.

Actually the historical and ancient DNA evidence both point to the fact that East Asian ancestry arrived in the last two thousand years. The spread of the first Gokturk Empire, and then the documented shift in the centuries around 1000 A.D. from Iranian to Turkic in what was Turan, signals the shift toward an East Asian genetic influx. Alexander the Great and other Greeks ventured into Central Asia. The people were described as Iranian looking (when Europeans encountered Turkic people like Khazars they did note their distinctive physical appearance).

We have ancient DNA from the Altai, and those individuals initially seemed overwhelmingly West Eurasian. Now that we have Scythian ancient DNA we see that they mixed with East Asians only on the far east of their range.

The second paper is very confused (or confusing):

The time divergence between Indian and European Y-chromosomes, based on the closest neighbour analysis, shows two different distinctive divergence times for J2 and R1a, suggesting that the European ancestry in India is much older (>10 kya) than what would be expected from a recent migration of Indo-European populations into India (~4 to 5 kya). Also the proportions suggest the effect might be less strong than generally assumed for the Indo-European migration. Interestingly, the ANI ancestry was recently suggested to be a mix of ancestries from early farmers of western Iran and people of the Bronze Age Eurasian steppe (Lazaridis et al. 2016). Our results agree with this suggestion. In addition, we also show that the divergence time of this ancestry is different, suggesting a different time to enter India.

Lazaridis et al. accept a mass migration from the steppe. In fact, the migration is to such a magnitude that I’m even skeptical. Also, there couldn’t have been a European migration to South Asia during the Pleistocene because Europeans as we understand them genetically did not exist then!!!

I assume that many of the dates of coalescence are sensitive to parameter conditions. Additionally, they admit limitations to their sampling.

Ultimately the final story will be more complex than we can imagine. R1a is too widespread to be explained by a simple Indo-Aryan migration in my opinion. But we can’t get to these genuine conundrums if we keep having to rebut ideologically motivated salvos.

Related: Ancient herders from the Pontic-Caspian steppe crashed into India: no ifs or buts. I wish David would be a touch more equivocal. But I have to admit, if the model fits, at some point you have to quit.

16 thoughts on “Indian genetics, the never-ending argument”

  1. While I myself commented in Swarajya against unfairly attacking Razib, I don’t think you genetics folks cover yourself in glory either. Consider (warning: I don’t know any genetics, and am going by common sense, and welcome corrections):

    1. Poznik is very clear that the Z93 splintering predates the end of the Indus valley civilization by a few centuries. Tony Joseph wants to portray the two periods as coinciding (so as to force-fit the scenario of violent invasion). Why this dishonesty? And why was Razib initially so unqualified in his praise of Tony?

    2. And given that the earliest dates for Z93 are well within the early mature-Harappan phase (namely, 2500 BC), and “splintering” took a few centuries, why should Razib have a “hard time imagining” anything but an invasion as he wrote on one of his earlier posts?

    3. Aryan invasion theorists circa 1500 BC (started moving from Russia in 1800 BC) as the entry period of Aryans (if I remember Witzel . And yet no one points out that they were spectacularly wrong in spite of having been afforded the most prestigious academics positions and facilities; you pretend that you are in complete agreement with them, and focus you energies on hammering those who don’t have academic muscle. The powerful establishment ganging up against the commoner?

    4. Davidski attacks Swarajya for “abusing” Razib, yet the language of Swarajya is far milder, far less condescending than Davidksi’s. That guy’s rhetoric is reminiscent of all that has gone wrong between liberals and conservatives in US today.

    5. And frankly, as silly as this may sound, even a small act like RT-ing link to Tony Joseph by a murder-apologist like Audrey Truschke who tries to derive as much mileage as possible by unnecessarily poking Hindus in the eye is not going to endear you to Hindus.

    Someone had observed that scientists ganging together against Trump did not affect Trump as much as the credibility of the scientific establishment. Similarly, the institutional ganging up against those who feel for the Hindus might well hurt the credibility and popularity of genetics community in India.

    You guys can do whatever you are doing in a more level-headed manner. Else you and us risk going the way of liberals and conservatives in the US.

    1. murder-apologist like Audrey Truschke

      can you tell me about this person? i have no idea who is is.

      i’m not too focused on the 1500 BCE date. i think joseph’s language was a little inflammatory probably in context. but to be honest that seems to be the indian way judging by some of the commenters i get. am i wrong? (basically a lot of hyperbole no matter their position)

      also, the reality is that joseph does generally align with the science even if he is shoehorning things. a lot of stuff out of india now basically inverts facts and obfuscations. so honestly it’s an improvement

      i have submitted something to *india today*, so i will put my own piece out there.

      1. Thanks very much for responding.

        Sorry for assuming that you knew who Audrey Truschke was. Just to answer your question, that comment referred to your retweeting this:
        The background is that Hindu-sympathizers including myself view Truschke as an apologist for Aurangazeb, who for the sake of popularity writes inflammatory rationalizations for his actions (e.g., the claim that Aurangzeb executed Guru Tegh Bahadur for fomenting unrest).

        But given that you didn’t know who she was, I withdraw that point, which no longer stands.

        (BTW it was the linguistic “evidence” which Truschke speaks of and you retweeted, that the original AIT guys used to put the migration at around 1500 BC.)

        I can see that there is more “tautness” to the reasoning in Joseph’s piece than most Indian articles. Which happens to also be what frustrates me – the resulting credibility enables him to slyly and believably throw in bits of propaganda here and there.

        Thanks again.

    2. also, in defense of davidski’s tone, his comments are a little out of control IMO, and tend to induce some sneering. i’m pretty sure i know who he’s talking to, and it’s not hindu nationalists, but a specific commenter.

    3. @froginthewell

      The signal of the major expansion in South Asian Z93 Y-chromosomes does predate the end of the Indus Valley civilization, but you need to consider that the Pontic-Caspian steppe is far from South Asia, so if the expansion of Z93 started there, it would take a while to get to South Asia.

      In other words, the history of Z93, wherever it happened, is going to be recorded in modern-day Z93 sequences wherever they are today, and that includes India or, say, New York.

      And yes, I do get carried away sometimes, and I’m also often condescending when it comes to these issues, because despite all of the data that we now have, which clearly is pointing to South Asia being overrun by Bronze Age steppe herders, a lot of people refuse to get it. Generally I’m a patient guy, but I feel like I’m up against some sort of group-originated disorder here.

      1. but you need to consider that the Pontic-Caspian steppe is far from South Asia, so if the expansion of Z93 started there, it would take a while to get to South Asia.

        The relevant sentence from the paper seems to be: ” In South Asia, we detect eight lineage expansions dating to ~4.0–7.3 kya and involving haplogroups H1-M52, L-M11, and R1a-Z93 (Supplementary Figs. 14b, 14d, and 14e). The most striking are expansions within R1a-Z93, ~4.0–4.5 kya.” – to me this reads as the expansion having started in South Asia; please let me know if I am misinterpreting.

        Regarding those people who “refuse to get it” – while I am sorry if you received unfairly hostile attacks, you might find some of that understandable, though not acceptable, if you could see where those people come from; for them this issue is mixed up with several issues of contemporary Indian politics that concern and frighten them, which would be a digression to elaborate. Yes, they should emotionally disentangle themselves from such concerns when they read you, but sometimes it is humanly difficult. As an analogy you could consider how someone not familiar with western politics or recent history might find James Watson’s forced retirement or Tim Hunt’s firing ridiculous; yet it was political baggage and not any cold reasoning that drove these decisions.

        1. to me this reads as the expansion having started in South Asia; please let me know if I am misinterpreting.

          z93 is found outside of india in central asia, in the altai, and in ancient remains from the pontic steppe (sbruna and scythians). all seem subject to this expansion. it most definitely expanded in india, but it expanded elsewhere too. so it is part of a simultaneous process.

          if it expanded out of india then it is strange that there is no evidence of ASI in the northern z93 populations. it could be that ASI and ANI were segregated for tens of thousands of years in south asia; remember, ANI is rather close to west asian and central eurasian populations. but ASI is closer, though very distantly, to east eurasia groups. this is a genetic gradient that is like the himalaya today.

          in contrast, we do see all the constituent ancestries from west asian and central eurasian groups in modern indians, to some extent. that is, there is ANI+eastern farmer+WHG (via EHG). the distribution varies by caste and region in a manner which aligns with the autosomal admixture cline.

          the model of intrusion of ANI from outside within the last 10,000 years is far more parsimonious. that does not mean it is correct; ancient DNA will be definitive on this.

          a simpler way to say it is this: south asians can be modeled genetically complex mixtures of groups to the west and north. groups to the west and north can not be modeled as genetically complex mixtures of south asians.

          1. I didn’t mean to comment that Z93 expanded only out of India; I was referring to my reading of a sentence in Poznik etal that the specific splintering of Z93 dating to 4.5 kya that they talk of in the paper, was supposed to have happened in India (that is how I read their sentence; but my reading could be wrong or their phrasing could be ambiguous). Because 4.5 kya is the earlier half of mature Harappan era, and if instead as Davidski suggests the splintering originated in the Pontic-Caspian Steppe and reached Harappa towards the time of its decline, that would have different implications for the invasion vs migration question.

            Thanks for the additional explanations. If Joseph’s article had any causal contribution towards your writing in India Today, that would be a good thing to have come out of it.

        2. As an analogy you could consider how someone not familiar with western politics or recent history might find James Watson’s forced retirement or Tim Hunt’s firing ridiculous; yet it was political baggage and not any cold reasoning that drove these decisions.

          i have been thinking recently about these sorts of analogies. yes i agree.

        3. froginthewell,

          Thanks for a sane and coherent summary of all the baggage. I tend to think that most of the resistance is not to the idea of immigration/invasion from elsewhere, rather to the dating of the event and how linguists went about it (Talageri-Witzel brouhaha) before geneticists arrived. And now people want to throw out the baby with the bath water.

          Future may yet have some surprises for us, and truth will come out in its own time.

          1. This geneticist vs linguist (and various kinds of historians) distinction is a great observation. I have never seen geneticists try to derive legitimacy from how just their cause is or how (so many of) their critics are trolls. In other words, they are legitimate scientists. Witzel too (though not Doniger, and only partially Thapar) fits the description of not playing politics as a means of justifying theories, but ultimately the usual social “sciences” history-types are all attached to their pet conjectural formulations which lack the falsifiability that makes science science.

            So, the Hindutvavadis (namely, my side), by clubbing geneticists with linguists and historians, do a disservice to their side by elevating a Doniger’s voodoo “analysis” to the status of a genuine science like genetics. In addition to acquiring bad reputation, that is.

            I too share the hopes for future surprises. And in the shorter term, look forward to the India Today article.

  2. The Wrath of Khan – “the day will come when all the ledgers will be balanced.”

  3. Thanks for the additional explanations. If Joseph’s article had any causal contribution towards your writing in India Today, that would be a good thing to have come out of it.

    actually it was months in the making.

  4. Razib, I am pleased to see that you have kept your options open. You seem to change your options as soon as new evidence is placed before you. I have seen you flip flopping depending on the strength of the evidence, at that particular moment in time . This shows an agile and very less biased mind without some pre-determined notions ruling your judgement. Reminds me of Keynes, who said: When the Facts Change, I Change My Mind. What Do You Do, Sir?

  5. Indian R1a is mainly R-L657 and as per Y-full it is about 300 years younger than R-Z93.If R-Z93 is 5KY old (as per Y-full tree)and as the oldest R-Z94 found at potapovka ,it is highly probable that R-657 aroused at least not in South Asia.The picture will be clearer if R-L657/Z2123 is further studied with it’s associated mtdna & auDNA.

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