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Thread: The genetic origins of the Indo-Iranians and greater South Asia1139 days old

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    Default The genetic origins of the Indo-Iranians and greater South Asia

    In this thread, I aim to discuss, and even possibly reach a partial conclusion regarding the genetic affinities of the ancient Indo-Iranian people. As far as I am aware, we haven’t ever had a proper discussion on the genetics of the Indo-Iranian groups. What has been stated since the very debate of Indo-Iranian origins began, however, is that the term Aryan was falsely used by the Nazis, when it was in fact an ethonym that was used by the aforementioned Indo-Iranians, particularly the Sanskrit-speaking Vedic people of South-Asia and the Persians. Present linguistic sub-sets include the Indo-Aryan, Iranian, Dardic and Nuristhani speakers. While data from the Indo-Iranian speaking lands, and I refer to the area from the Iranian plateau to Bangladesh; is sparse, especially as far as South Asia proper is concerned, there are some general trends that have been discernible, thanks to the seminal paper on South-Asian genetics; Reconstructing Indian population history and after-market, genome blogger projects such as the Harappa Ancestry Project, Dodecad Ancestry Project and to a lesser extent due to it’s main focus being outside of our area of interest i.e Europe, the Eurogenes Biogeographic Ancestry Project. I will attempt to view each region in brief.

    South Asia

    So, what do we know about South Asia as of now? For starters, the aforementioned paper by Reich et al told us that South Asians are largely a mix between two ancestral groups, one a component that is interchangeable with most main-stream West Eurasian groups – termed Ancestral North Indian and the second, a group with little affinities in a Eurasian context, but slightly more related to East Eurasians than West Eurasians – the Ancestral South Indians. The ASI’s marginal affinity with East Eurasians as opposed to West Eurasians might well explain why the 23andMe’s ancestry painting seems to overestimate the West Eurasian admixture for most South Asian individuals – much of the actual ASI admixture is being recognized by 23andMe’s ancestry painting as European, while the rest of the ASI is being assigned to the Asian component – if we were to form a correlation between inferred ANI-ASI and European-Asian scores for any given individual, the ASI is usually assigned to the Asian component slightly more than it is to the European component. This is perfectly consistent with the aforementioned notion that the Ancestral South Indians are fairly distinct from both East Asians and West-Eurasians, but having more affinities with the former.

    There are also a few elements that fall outside of the analytical algorithm. I am primarily using the HAP’s K=11/Reference III Ks for reference. The first is a component associated with Near Eastern populations and the second, Northern European populations; seen as SW Asian and (Northern) European respectively. Razib Khan, author of the Gene Expression blog has tentatively lumped these two elements under the term ANI2, given it’s close relationship with ANI, but comparatively exogenous nature. In regular ADMIXTURE runs, we see that South Asians are characterized by mainly the South Asian, West-Asian [Balochistan/Caucasus over at HAP’s standard K=12 and just Caucasus in Eurogenes’ West-South-Central Asian admixture run] and East Asian components.

    The West Asian admixture is elevated among North Western ethnic groups, and peaks among the Pathans. South Indian Brahmins have an appreciable chunk of this, as do the forward caste Reddys of Andhra Pradesh, but to a much lesser extent. Some ethnic groups also tend to have Northern European admixture, mostly Eastern European admixture which is generally around 5% among Dravidian speaking Brahmins and around 10-15% among North Western South Asians (Pathans and Punjabis, and to a lesser extent the Sindhis) and the Brahmins of the Gangetic valley or as some like to call the area, the Hindi belt. The European is slightly more elevated in HAP’s K=11 for most participants who already exhibited the same in previous runs, and is usually biased towards European as opposed to SW Asian for these participants. The SW Asian peaks among the Keralaite Nasrani (Syrian Christian) participants as far as India is concerned, as is consistent with their claimed ancestry. Otherwise, most non-Brahmin Southern Indian castes exhibit some SW Asian, but almost no European. The Reddys exhibit a fair amount of SW Asia in comparison to generic South Indians, but once again almost no European.

    The other non-West Eurasian intrusive element is the Mundari substrate, found mainly in the Eastern parts of India, such as among Bengalis and the Austro-Asiatic tribes of the Chota Nagpur plateau, which explains these populations’ pull towards Eastern Asia, attested by the substantial amount of East Asian admixture as opposed to mainland South Asian populations; who usually have no more than 0-3% of the same. Likewise, the Brahmins of Eastern India, specifically Bengal tend to have a sliver of East Asian admixture absent for most Brahmins otherwise, indicating that just as in South India, there was admixture with the locals to an appreciable extent. These Brahmins however, generally tend to be far more European than SW Asian, and notably more European than their Dravidian speaking counterparts in the South.

    One big assumption we’re making here by quoting these ADMIXTURE run(s) for making inferences regarding population trends and the like is that the patterns observed are not selective novel patterns we are seeing at any given particular level of K and with that particular reference data-set.

    Afghanistan

    There seems to be no Autosomal DNA data on the various ethnic groups of Afghanistan, assumably due to the political atmosphere of the country, which has in turn prevented academics and geneticists from obtaining samples for testing. The Pashtun Pakistanis exhibit among the highest West Asian and Northern European scores in the sub-continent, apart from the Kalash for the latter. I reckon this may be an indicator of the general mix of Afghan Pashtuns, if not an indicator that both those components might even be comparatively elevated among them. The second question is regarding ASI among Afghan Pashtuns – other Iranian people generally lack this component, but could it be present among Afghan Pashtuns considering their proximity with populations that do exhibit the same?

    Iran

    I’d like to make it clear that I am just an enthusiast and a spectator regarding population genetics in general, but more so regarding the genetics of non-South Asian groups. I am however, far more familiar with Iranians than say, West-Africans, but not as familiar with them as I am South-Asians. Dienekes Pontikos’ ANI-ASI Zombie exercises revealed that the South Asian component of Iranians was more ANI than ASI.

    The Iranian reference data-set (Behar et al?) turned out as ANI – 11.7% and ASI- 7.5% and the Dodecad Iranians (Iranian_D) was ANI – 12.0% and ASI – 6.9%. A point to note is that the “South Asian” component we see in ADMIXTURE exercises is usually more ASI than ANI, at least in the case of most subcontinentals. My question is – do Iranians really have ASI admixture? If this was absolutely certain, it would certainly bridge some gaps in terms of continuity – it is not totally implausible for ASI admixture to peak in South and East India and thereon have a geographic cline reaching up to Iran i.e diminishing as we go further West, but I’m not so sure, since Iranians, as far as I’ve observed tend to exhibit some North East Asian admixture, but are overwhelmingly West-Eurasian otherwise. I was always under the impression that the South Asian admixture among Iranians is Indo-Iranian specific and entirely affiliated with the Ancestral North Indian component. As an aside, observers have suggested that Doron Behar’s Iranian sample is actually from either Khuzestan, Balochistan or Hormuzgan/Bandar Abbas considering the presence of African admixture which is atypical for generic Iranians. Considering ASI’s East-Eurasian affinity – is the software inferring the same NEA admixture among Iranians as ASI instead i.e is this just an artefact of the program attempting to fit the Iranians into the available ancestral populations?

    Who were the Dravidians?

    I’d like to discuss this at length some time later into the discussion, but not now. As of now, summarizing the various theories of genome bloggers, genetics enthusiasts, linguists, academics and archaeologists, it seems that the Dravidians might either be:
    - A farming group from the Middle East, perhaps with ties with the Elamite civilization that had Harappa face an influx of agricultural revolutionaries, who spread their genes in the form of the main West Eurasian admixture in India and Dravidian languages.

    - A pastoralist group that was preceded by a farming population in the Indus valley perhaps represented by the Burushaski or Nihali languages, and virtually entirely replaced these languages with their own. This might also explain why ANI and ASI is present all over the subcontinent and well synthesized – Diogenes suggests that some of the mainland ASI may have developed a crop technology independent of the ANI farmers, yet SW Asian is has a gradient of sorts. Hence, in light of this I reckon the two groups may have intermingled with each other to a large extent, resulting in the mixed West Eurasian-ASI populations of the present day Indian sub-continent. As for SW Asian, the component is stratified along region, and is fairly prominent in Sindh, and finds an appreciable frequency among forward caste, socially dominant, yet historically caste Shudras in South India like the Reddys of Andhra Pradesh. This might imply that the advent of the Dravidians was another case of elite dominance genetically, albeit less so than the Indo-Aryans.

    - Simply a local development.

    What do the Balochis/Makranis and Brahui represent for the greater South Asian genetic canvas?

    There are a few main, albeit rough clusters in South Asia, and the Balochi and Brahui comprise of one of them. They are characterized by their high West Asian admixture. The Makrani are southern Baluch with some African admixture. The Brahui are the sole Dravidian speaking group of the area, which might suggest that Dravidian languages dominated the area before the advent of the Indo-Aryans. The high West Asian admixture is understandable for the Balochi, as it seems that the Balochi language was spread by relatively recent migrants from the Western portion of the Iranian belt. Brahui vocabulary on the other hand apparently also has Western Iranian contribution in specific, but mainly Dravidian. I have always found it rather strange that two groups who are linguistically different would be so similar to each other. Reading this paper it seems that the Baloch identity is more political and tribal; and far more fluid as opposed to the fanatically lineal Pathans of the same area and it's whereabouts. It is somewhat implicative of the fact that many Brahui were assimilated into the Baloch identity or perhaps less likely, the Brahui have a lot of admixture from the Baloch. I am a little confused here, so a little chiming in would be most appreciated.

    The Indo-Iranians and the Dravidians: What were their ancestral components?

    I have often suggested that the Northern European component in admixture breakdowns found among S-Asians may not be a clear-cut diagnostic marker for the Indo-Iranians. Rather, they might show up in ADMIXTURE as a population with a mix of both European + SW Asian (again, in reference to HAP’s K=11). In related discussions, people have gone onto suggest that the original population might have a 2:1 mix of the two components as an upper bound.
    1.png

    SW Asian ancestry is plotted on the Y-axis; European on the X. A regression line runs through. The coefficient is .659 — suggesting a 3:2 mix of European/SW Asian seems right.

    If you notice, all the groups that are traditionally believed to descend from the Indo-Aryans (and often believe themselves to be so), but more realistically speaking, probably have a substantial amount of ancestry from the ancient IE-speaking warrior-herder nomads tend to have European scores that trump the SW Asian scores. The table below has some examples to illustrate the same. This even seems to hold water for the Dravidian-speaking upper castes, such as the Tamil Brahmins (8% SWA and 10% EU), although the difference between the two components is lesser than for NW IE groups, and lesser in terms of numbers in general.
    Code:
     Ethnic Group  	  SW Asian     European
              Kalash	               11%	     22%
              Pathan	               17%	     19%
              Sindhi 	               15%	     19%
              Kashmiri	               13%	     17%
              Punjabi	               12%	     17%
    However in other admixture runs, the West-Asian admixture trumps the NEU admixture by quite a bit. I would appreciate opinions as to why there is such a difference across these different types of runs, especially considering HAP's K=11 has a robust reference data-set from a South Asian POV.

    Moving on, on the other hand, non-Brahmin Dravidian castes consistently seem to be biased towards SW Asian than European, with a negative correlation between the two to add to that, once again, plotted. Clearly, this is consistent with the fact that while generic South Indians do have West-Asian admixture on say, the regular Dodecad K=10 results, they usually lack any European admixture.
    2.png
    Credit – Thorfinn of the Brown Pundits blog[1][2]

    So my question is – What components do you think the ancient Indo-Iranians carried and at what proportions?

    Some of you may have been following Dienekes’ Zombie admixture exercises. Two posts to note in light of this topic:
    1. How to create Zombies from ADMIXTURE
    2. Analysis of HGDP Pakistan groups

    The results for the Pakistani populations seem nothing out of the ordinary except for the Kalash – in the first run, they seem to primarily be a mix between the West Asian and South Asian components. In the second run, they are almost entirely West Asian, with a sliver of ASI admixture. What makes me a little suspicious of this run is that the Kalash have, as Dienekes mentions, as much ASI as the Behar et al Iranians and Iranian_D of his Zombie run, but no Ancestral North Indian admixture. How on earth did the Kalash end up mixing with a population which was predominantly ASI upon their arrival in the Hindukush?

    Harappa Ancestry Project’s K=11 run for the reference populations revealed that the Kalash were-
    1. South Asian - 60%
    2. East Asian - 3%
    3. South West Asian - 11%
    4. European - 22%
    5. Siberian - 1%
    6. Papuan - 1%
    7. American - 2%

    The South Asian in this run is predominantly West Eurasian-like a.k.a ANI, and considering the complete absence of the Onge component (a cousin population of the original ASI), the Kalash's South Asian score of 60% is likely almost fully specific to Ancestral North Indian. The NEU admixture is double that of the SW Asian admixture – perfectly consistent with the 2:1 NEU:SW Asian ratio observed among Indo-European South Asians and upper castes. The East Eurasian admixture adds up to 7%, which is almost how much the Kalash exhibited ANI in the HDGP-Pakistan run (8.4%). Once again, my question is – is the so called ASI admixture among the Kalash simply an artefact of the software trying to fit them in with the available ancestral populations? Is it not far more plausible that the Kalash, like, say, the Burusho have actual East-Asian admixture? Now it beats me as to how an East Eurasian population found its way to the Hindu Kush, but this is attested, as far as the Burusho are concerned by the presence of y-DNA C, O and Q and East-Asian admixture autosomally. But more to the point, it seems highly implausible to me that the Kalash have ASI admixture, but no ANI admixture. If they did mix with a group that preceded them upon coming to the Chitral area to a certain extent, it is more likely than not that the group was a hybrid ANI-ASI population, if not predominantly ANI like the non-Kalash locals of the are are now, due to comparative lack of proximity with ASI admixed populations (Pathans are up to 81% ANI).

    Is the overwhelming predominance of the West-Asian component a reflection of their rate of homozygosity, inbreeding and genetic isolation?

    I think it is telling that the Kalash exhibit NEU : SWA at a ratio of 2:1 at HAP/K=11; and the Pathans still retain this component even in this run – this is assuming that the original proto-Indo Europeans are in fact from Eastern Europe. If I’m not wrong, even Northern Europeans exhibit some amount of West Asian admixture, almost the same amounts as North West South Asians exhibit Northern European admixture. To me, this open new avenues for speculation – where did the IE people originate? It looks to be that it could have been a case of elite dominance (but not forgetting the effects of recombination over time) in both areas, depending where the proto IE people originated. I am not quite sure as to whether I have articulated this correctly, but opinions on this are most welcome.

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    Unfortuanetly, ADMIXTURE is much too fickle for this sort of thing. The only sure way of answering these questions is via ancient DNA and some really powerful genome-wide segment analysis. I'm sure this will be done, and until then I'll let Dienekes hang himself. It'll be funny to watch.

    Only one Scythian (ie. Indo-Iranian) skeleton has been tested thus far for Y-DNA, and he was R1a1a. He also matched Russians and Poles best using just 6 autosomal STRs. The same, or perhaps another Scythian also had mtDNA N1a of an Eastern European variety.

    There's a detailed study being done now by Germans, comparing ancient Yamnaya DNA to those from various Scythian sites. That should be interesting, and I predict it'll show a movement of people from a staging point around the Volga and Samara, deep into Asia across the steppes. We'll probably see their markers in many modern Central and South Central Asians.
    Last edited by Polako; 2011-06-14 at 15:18.

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    Quote Originally Posted by Polako View Post
    Unfortuanetly, ADMIXTURE is much too fickle for this sort of thing. The only sure way of answering these questiions is via ancient DNA and some really powerful genome-wide segment analysis. I'm sure this will be done, and until then I'll let Dienekes hang himself. It'll be funny to watch.

    Only one Scythian (ie. Indo-Iranian) skeleton has been tested thus far for Y-DNA, and he was R1a1a. He also matched Russians and Poles best using just 6 autosomal STRs. The same, or perhaps another Scythian also had mtDNA N1a of an Eastern European variety.

    There's a detailed study being done now by Germans, comparing ancient Yamnaya DNA to those from various Scythian sites. That should be interesting, and I predict it'll show a movement of people from a staging point around the Volga and Samara, deep into Asia across the steppes. We'll probably see their markers in many modern Central and South Central Asians.
    The problem with this is that the Scythians are rather irrelevant when one talks of the Indo-Iranians and their origins, reasons being because their time in history is quite late when it comes to this topic, secondly they're not the only Iranic speaking group, and third, the Scythians at one point in history were considered a group of different peoples rather than a single ethnic group, meaning those calling themselves Scythians in western Russia were likely Slavic in origin for most part, not Iranian, but one would consider them Scythianized Slavs.

    I think the true origins of Indo-Iranians probably falls somewhere between the Andronovo and the BMAC, the Andronovo people were likely an Indo-European speaking people that fused with the BMAC natives and the Indo-Iranians were born, basically I think Southern-Central Asia is the home of the first Indo-Iranians.

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    Quote Originally Posted by Polako View Post
    Unfortuanetly, ADMIXTURE is much too fickle for this sort of thing. The only sure way of answering these questions is via ancient DNA and some really powerful genome-wide segment analysis. I'm sure this will be done, and until then I'll let Dienekes hang himself. It'll be funny to watch.
    Polako, I remember you had some criticisms regarding Dienekes' Zombie methods, but didn't quite elaborate. I would appreciate a few words on that. Also, if it's not too tedious for you, it'd also be great if you could post links/studies regarding the Indo-Iranians - archaeology, genetics, skeletal remains, etc. Or perhaps you could point me out to a few of your blog posts or threads you've created here. Thanks.
    Last edited by Vasishta; 2011-06-21 at 13:26.

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