by Alberto

West Iranian vs. East Iranian ancestry (with Vahaduo’s tool tutorial)

As you all know, there have been two aDNA papers released recently about Central Asia to North India. I didn’t dedicate a post to them (there are comments in the previous thread about them, though), mostly because the first one (The formation of human populations in South and Central Asia, Narasimhan el al. 2019) had already been extensively commented when the preprint was out, and while it did bring more samples these mostly add quantity to already sampled populations with few new ones (and not relevant enough to deserve a new post), while the second one (An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers, Shinde et al. 2019) finally brought the first ancient sample from within modern India, but it was only one low quality one that didn’t add much to the better quality “Indus periphery” ones already present in the former paper.

However, there’s still a bit of confusion regarding the ancestry to the people of the Indus Valley (and generally to the genetic structure of SC Asian populations), so here I’ll try to give some insights that might help to clarify the situation for further, better informed, analysis.

The basic premise here would be to split Iranian ancestry into West and East Iranian. The main difference would be the ratio of Basal Eurasian to ANE ancestry (higher in the west, lower in the east), but given the lack of Mesolithic samples we’re still unable to get the whole picture. However, some basic concepts can still help us to better understand the situation. So let’s start.

Vahaduo’s online modelling tool

And I’ll use his post to introduce a recently released online tool that deserves more attention, given its quality and usefulness. It’s been written by Vahaduo, with a similar purpose to my own Xmix, but more complete, faster and not requiring any local installation. So I’ll use this post to show how to use it for any of the readers to be able to try their own models and be able to test for themselves whatever they are interested in.

The first (and only) thing you’ll need is to get some datasheets that are valid to use with Vahaduo’s program. The best (and recommended) ones being the Global 25 scaled datasheets from Eurogenes. One will have all the individual samples and the other the averages of each population. Ones you have these, you can proceed to the site and start testing. Here we’ll go directly to test what I mentioned above: East vs. West Iranian ancestry.

For West Iranian ancestry, I’ll use the average of the Early Neolithic samples from the Ganj Dareh site in the Zagros mountains. And for east Iranian I’ll use the average of the easternmost samples we have so far: Sarazm_Eneolithic. So I’ll need to copy the coordinates of these in the “SOURCE” tab (one per line):

Now, two sources will probably not be enough to test the samples from SC Asia and Indus periphery, since there are more streams of ancestry in them (at least one related to ANF and the other to AASI). So I’ll go ahead and add the average of Barcin_N samples and the average of modern Onge and Naxi populations.

Then for the targets, I’ll use individuals instead. In this case I’ll start with the “Indus periphery” samples, which are labelled in the datasheets as IRN_Shahr_I_Sokhta_BA2 and TKM_Gonur2_BA, so again one per line I copy and paste them in the “TARGET” tab:

And now we’re ready to run the program and get the results. Since we’ve added multiple target samples, we should go to the “MULTI” tab and click on the “RUN” button, which will show us this:

As you see, Naxi doesn’t appear in the results, and that’s because all the samples got 0% ancestry from it. If we wanted to see all the sources in the output, we’d just have to click on the “PRINT ZEROES -NO” button (which would change to “PRINT ZEROES – YES”) and click “RUN”. The “AGGREGATE – YES” button is to aggregate the percentage of multiple sources with the same label (for example if instead of using the average of Ganj_Dareh_N we would have used all the individuals as sources, we would choose to either see the results with each individual specified or to aggregate them into a single column with the sum of them).

Then we can download a .CSV file to import it into a spreadsheet and make further calculations if needed (or for sharing purposes using Google Docs, for example). The “DISTANCE” tab is also useful to calculate the distance between a sample to all the sources (you could copy for example the whole datasheet, being careful not to copy the first row with the PCA labels) and get the top 25 closest samples/populations.

It just takes some minutes to get familiar with the program and the options so go ahead and try it. It’s definitely a very useful tool.

Some insights into SC Asian and Indus Valley ancestry

So let’s start with what we see in the above model of the Indus periphery samples. Leaving (for now) aside the fact that they may have some recent admixture from the places where they were found, one striking thing is the very variable ratios of West and East Iranian ancestry. In the following spreadsheet the above results can be seen (Sheet 1) together with a second run with the 100AHG simulation provided by Matt in the previous thread (Sheet 2), and in both the the calculated ratio of West to East Iranian ancestry. It’s easy to see that there is no correlation between that ratio and the amount of AASI in each sample, which makes it irrelevant for this matter whether they have any admixture from the local populations or not. Either way, we’re seeing a diverse population not just in terms of AASI to West Eurasian, but in the more sutle, but still important, West to East Iranian ancestry.

This pattern of significantly different ratios in West and East Iranian ancestry is equally seen in the regular Shahr-I-Sokhta BA samples (Sheet 3) and in the Turan Eneolithic samples (Sheet 4). The Iranian-like ancestry in the Indus periphery samples is therefor very similar to the one in those places. But they’re not all homogeneous, and point to mixed populations with probable input from West Iran. Modelling the samples with more proximate sources and using the 100AHG simulation again, it looks like this:

And using the sample with the highest amount of AASI as a source instead of the 100AHG simulation, something like this:

So what does this mean? First that things are a bit more complicated than getting the average of a population and building a tree estimating the divergence time from another one under an assumption that there is no admixture between them just because they’re not the same. In more simple words, we can’t really know with certainty if there was some migration from the Zagros Neolithic to North India or if there was none. Both options are possible. What we can say, though, is that we’re talking about a significantly different case to the Neolithic transition in Europe, since there must not have been a large replacement by outside farmers in any case.

All of this opens some interesting questions regarding the genetic history of South Asia. Unfortunately, we don’t have the data to give any answer to those questions, but it’s still worth knowing them and the different possible answers. For example:

  • Who were the Mesolithic Hunter-Gatheres from North India?
  • Who were the first farmers?
  • Was there any subsequent migration before the Bronze Age?

Let’s break up the genetic structure of (putative) IVC samples into the 3 main streams of ancestry:

  1. AASI
  2. West Iranian
  3. East Iranian

This does not mean necessarily three different populations. Two or more of these ancestries could have been already mixed since very early. But let’s examine the possibilities:

First, a basic look at the geography of India tells us that there are no major barriers within it, compared to the big barriers with the outside. This makes less likely he possibility of two extremely different populations during the Mesolithic living in South and North India, and the one in north India being almost identical to the ones outside (Iran and Turan). It could be (only aDNA can tell us), but it looks like the least parsimonious.

Together with the diversity in the ratios of those 3 streams of ancestries, it’s really unlikely that we could be talking about an isolated India-specific population. We have to think in terms of some degree of migration to India from outside before the Bronze Age.

The possibilities about who was where at each point in time are many, and I won’t argue for any of them. It’s speculative at this point. But as possible examples:

We could have a AASI-rich population, but with significant East Iranian ancestry too during the Mesolithic. Then we could have a moderate migration from the Zagros Neolithic and no more migrations up to the IVC time where we have samples. This would be somehow similar to the Neolithic transition in Turan, where presumably a mostly East Iranian population was there in the Mesolithic and received some migration from West Iran during the Neolithic transition. The difference (apart from the lack of AASI ancestry in Turan), is that the communication between West Iran and Turan is easier, and gene flow continued (both ways) throughout the Chalcolithic and Bronce Age.

The problem with this scenario is how to explain the presumed differences in levels of AASI in the IVC and their lack of correlation with the East Iranian ancestry that would have been associated with it.

Scenarios were we separate the three streams of ancestry could better explain the situation, though given that Turan Chacolithic had already a diversity in East and West Iranian ancestry ratios that could serve as a single migration too (note that neither West Iran Chalcolithic or Turan Bronze Age would fit well as admixing sources due to their excess of ANF-related ancestry). I’ll leave to the comments any further variations within these constraints.

The Steppe ancestry in Turan and North India

This subject has already been discussed everywhere in great detail, for a very long time. So I didn’t plan to look at it again. I don’t have much more to say, but I’ll go through it fast.

The post BMAC samples that we have hardly show any steppe admixture. In the same spreadsheet linked above (Sheet 5), I’ve added the samples with an average date in calBP of  <3700 years in descending order (note that the Present is defined as 1950 CE, so you’d need to add 69 years to get the real BP as of today). There’s one Parkhai_LBA_outlier (1497-1413 calBCE) that shows 9.2% Sintashta_MLBA admixture. The rest until the last BA samples (3250 BP) are in the noise levels. It’s only the single Iron Age sample from Turkmenistan (912-799 calBCE) that has a big increase to 50%.

In the Swat Valley, we have the earliest samples from the period 1200-800 BCE. They have significantly more steppe admixture, ranging between 20% and 0% and an average of around 10%. The variability of the amount of steppe ancestry doesn’t seem very compatible with their estimate of admixture happening 26 generations before in that same place, in that same population. But the shortcomings of their observations that provide evidence of the arrival of steppe ancestry to South Asia in the first half of the second mill. should have been already evident without looking at individual variability with up to 0% levels.

Another of the inferences for supporting such evidence was their observation that after he MLBA the steppe got Siberian/East Asian admixture, which is not found in modern India. However, they could model modern population using the Kangju samples from Kazakhstan (II-V CE). Modern samples are never a good way to make inferences about prehistory (including modern frequencies of certain uniparental markers). It seems rather arbitrary why would populations choose Sintashta or Kangju (though maybe Kshatriya ones make sense),

or indeed why would they choose Sintashta_MLBA or the Kashkarchi_BA samples from 1200-1000 BCE which are almost identical,

or even adding the Turkmenistan_IA sample mentioned above too as a source (as suggested in the comments from the previous thread), which further splits the steppe ancestry in a relatively random way.

Overall not much to add about all of this steppe part. We’ll have to wait to see those samples from the first half of the second mill. BC around the Punjab before we can know with certainty how all this went.

 

 

 

164 thoughts on “West Iranian vs. East Iranian ancestry (with Vahaduo’s tool tutorial)”

  1. Thanks Alberto. Vahaduo’s modelling tool is cool. I myself, won’t try and tackle the complexities of the present-day Indian population structure, instead using two of the simulations I generated and ancient pops, I’ll look at the InPe and Swat/PAK_IA:

    #1: Modelling Indus_Periphery, then Swat, using my 0AHG and 100AHG sims and a set of later steppe and Central Asia populations: https://imgur.com/a/8YgJvPg

    (The set of pops in this scenario was: KAZ_Kumsay_EBA, RUS_Sintashta_MLBA, TJK_Dashti_Kozy_BA, RUS_Catacomb, KGZ_Aigyrzhal_BA, KAZ_Kangju, TKM_IA, IRN_Hajji_Firuz_BA, IRN_Hajji_Firuz_IA, IRN_Hasanlu_IA, IRN_Tepe_Hissar_C, TKM_Gonur1_BA_o, TKM_Gonur1_BA, IRN_Shahr_I_Sokhta_BA1, IRN_Ganj_Dareh_N, 0AHG, 100AHG, Gonur2BA, Shahr_ISokhta2BA. I didn’t realise about the “Show zeros” button so some won’t show up in runs, but they are being tested.)

    Indus_Periphery individuals fit fairly well as a composite of the 0AHG and 100AHG, though in fairness I did not use much of a range of Central Asian Neolithic pops, and some fit better than others, and Alberto’s analysis is quite probably the superior one on this.

    The Swat_IA set largely seem to show a preference for Kumsay_EBA+Kangju on the steppe side, and other than that not much unity. Kumsay are largely a combination of WSHG with a dose of Steppe Piedmont ancestry about 55:45, while Kangju are a later complex composite of largely the typical Steppe_MLBA (European Corded Ware like) ancestry with Turan and some low level of East Asian ancestry.

    Only the outliers Loebanr_IA_o:I12138 (who also takes a chunk of Aigyrzhal) and a sample I label PAK_Saidu_Sharif_H_o2:I6893 who seems to me to be an outlier, seem to need direct Sintashta / Sintashta like Dashti-Kozy ancestry, while others largely prefer Hasanlu_IA and Haji_Firuz_IA to pick up anything which Kumsay+Kangju doesn’t cover. On the “southern” side they don’t clearly prefer the 0AHG sim over various real pops.

    #2: Putting 0AHG in competition with the real Indus_Periphery set: https://imgur.com/a/uYJO4k1

    It seems that the 0AHG sim is universally dispreferred to the real Indus_Periphery pops (does not contribute). However, some populations do fit with some degree of better combining my AHG sim with real Eastern Iran+Turan populations, rather than use the real Gonur2 / Shahr_I_Sohkta2.

    The dominant proportions of the steppe related ancestry from Kumsay+Kangju seem pretty robust to including the real Indus_Periphery.

    #3: Removing both my sims: https://imgur.com/a/wi86pPT
    That tends to swell Shahr_I_Sokhta2 as the biggest potential contributor of AHG/AASI. It also results in a slight rebalancing of ancestry from Kumsay->Kangju, but largely doesn’t change too much.

    (#4: Though I hadn’t planned to do this when starting this post, some modern “cline terminal” populations, by no means an exhaustive analysis – https://imgur.com/a/2abV0pv. Most populations tend to swerve for IRN_IA / KAZ_Kangju_IA / TKM_IA contributors over direct Sintashta ancestry, except of Ror who get a relatively good fit with it, and Balochi and Brahui who seem to like a composite of relatively direct Ganj_Dareh with some Sintashta related, as well as a dose of Iran_IA, and are relative resistant to the 0AHG sim that represents an idealised Indus_Periphery_West with 0AHG.)

  2. “In the Swat Valley, we have the earliest samples from the period 1200-800 BCE. They have significantly more steppe admixture, ranging between 20% and 0% and an average of around 10%. The variability of the amount of steppe ancestry doesn’t seem very compatible with their estimate of admixture happening 26 generations before in that same place, in that same population. But the shortcomings of their observations that provide evidence of the arrival of steppe ancestry to South Asia in the first half of the second mill. should have been already evident without looking at individual variability with up to 0% levels.”

    Totally agree. Their 2000-1500bce dating for steppe entry into NW south asia, along with the idea that the steppe folk chose to skip BMAC on their route seems very random.
    If you plot the location of R1a and their radiocarbon dates on a map for Iran, Uzbekistan, Turkmenistan, Tajikistan, Kazakhstan, Uzbekistan, Pakistan – you will see a clear path from North to south starting around 2000bce in North Kazakhstan to 1400bce kokcha uzbekistan, to 1200bce kashkarchi, uzbekistan to couple of samples in 1000-800bce swat valley.
    There is one kokcha, south uzbekistan R1a sample which is poorly dated 2500-1500bce, but maybe thats closer to 1500bce as the other r1a sample from same place is dated 1400bce.

    They use ALDER admixture dating to push forward their point of a 2000-1500bce entry, but it seems to me that the R1a dominant male population entry into south asia could be rather late.. otherwise it looks like a female mediated entry in the samples found so far.. we do find 3 steppe women in dashty_kozy dated to 1500bce on their way south.

  3. @ Alberto

    With regard to Neolithic South Asia, it is hard to have solid opinions, even if at present I find the suggestion that Farming has a completely native origin in north India somewhat surprising. Did you note that Hotu Belt Cave sample has now been dated to 10,000 BC ?
    And in your analogy- ”What we can say, though, is that we’re talking about a significantly different case to the Neolithic transition in Europe, since there must not have been a large replacement by outside farmers in any case.” I would point out that this is not in fact the case, despite academic papers making such a claim. This is because such views are based on looking at LBK, who are the immigrants (from the Aegean) which moved into their own niche which was initially sparsely populated by HGs; followed by 2-phase miscegenation

    As to the ‘steppe ancestry progession’ in South Asia, I agree that some of the claims are unconvincing. Instead, the impact should be understood in at least 2 mechanisms.:

    1) initial contact between steppe pastoralists & BMAC groups c. 2000 BC
    – this was limited & ritualised
    – mostly female mediated (as we see no R1a in BMAC chiefs)
    – related to a diverse range of steppe groups incl. Dali-EBA-like, to Yamnaya like to Andronovo like. These would have been all quite distinctive linguistically & culturally, so they cannot be conflated under one rubric.

    2) Then we see the actaul ‘spillover” beginning after 1500 BC, with an actual range expansion of steppe pastoralists predominantly of the Sintashta-derivation , moving beyond their initial territorial domains.

  5. Yes, the data about the steppe progression that we have so far is what it is, and not what it’s said to be. We’ll see with further data.

    The Neolithic is not too well researched so far in South Asia, at least as far as I know (maybe there are more works not published in English yet, or that I just don’t know about), so it’s hard to say much. But it’s still a fundamental part of the history and so I wanted to start with some preliminary observations about it. The transition to the Neolithic and the transition to the Chalcolithic (which seems to take off rapidly and we soon find a large civilization emerging) are two very interesting subjects.

    @raj

    Yes, there are some mountains all over central India, but do you think they are major barriers for more or less continuous contacts? The word may mean “obstructor”, but this is what the link to Wikipedia says:

    The Vindhya Range (also known as Vindhyachal) (pronounced [ʋɪnd̪ʱjə]) is a complex, discontinuous chain of mountain ridges, hill ranges, highlands and plateau escarpments in west-central India.

    What is your take in this matter? Do you think that AASI-rich populations of hunter-gatherers were confined to the south until the Chalcolithic/EBA when thy started to move north and overtake the fully West Eurasian farmers from the north? That seems a strange proposal, no?

  6. “What is your take in this matter? Do you think that AASI-rich populations of hunter-gatherers were confined to the south until the Chalcolithic/EBA when thy started to move north and overtake the fully West Eurasian farmers from the north? That seems a strange proposal, no?”
    Although I wasnt asked, Id like to put forth a few points. Thanks.
    Before the rakhigarhi sample was published, the widespread consensus was that AASI dominated the north of India. However, the rakhigarhi and Indus periphery samples are Indian_IranN dominated, rather than AHG/AASI. This should be the first setback to the consensus and make them reassess.

    Also, there is hardly any ancient population in the north that needs to be proximally modeled with AHG as source. some indus_periphery sample + steppe_mlba is good enough for most swat iron age pops. so there’s no need for extra AHG between 2500bc rakhigarhi and 1000bc to model the swat valley populations. correct me if Im wrong here. this is what Im basing my claim on –

    “We next characterized the post-2000-BCE Steppe Cline, represented in our analysis by 117 individuals dating to between 1400 BCE and 1700 CE from the Swat and Chitral districts of northernmost South Asia (Figs. 2 and 4). We found that we could jointly model all individuals on the Steppe Cline as a mixture of two sources, albeit different from the two sources in the earlier cline. One end is consistent with a point along the Indus Periphery Cline. The other end is consistent with a mixture of ~41% Central_Steppe_MLBA ancestry and ~59% from a subgroup of the Indus Periphery Cline with relatively high Iranian
    farmer–related ancestry ”

    On the other hand, the richest AASI group is still 40% Indian_IranN. This leads to the speculation that Iran like ancestry wasnt restricted only to the north either.

    All in all it conveys to me that pure AASI was scant in the north in 5000bce, probably existed from Madhya pradesh (below vindhyas) till south during that time.

  7. ancient indian literature is pretty clear about the divide and there is no evidence of linguistic replacement north or south even with all the genetic mixing

    south indians likely had oversea links from sumer to indonesia possibly australia very early so nobody confined or overtaken either

  8. Interestingly, the islanders of the Persian gulf sampled in the new Iranian study plotted close to present day North Indians. There seems to have been a complex population dynamic along the gulf starting in the Neolithic – the region seemingly connected all the early centers of civilization in Eurasia.

  9. @A

    Yes, I think the consensus you mention about North India being what was then called ASI (now AASI or AHG-related) until after 2000 BC was totally unrealistic, and already proved wrong with the first samples that came in with the Narisamhan preprint.

    But let’s leave that behind and think in realistic terms. During the Harappan period it seems that there was still a significant variation in the levels of West Eurasian and AASI. This means that there were two different populations still admixing with each other. At some point back in time, these two populations would have been exactly that, two different populations. Who lived where? Who were the first farmers and who the hunter-gatherers? Did the Neolithic bring migration from outside India? And the Chalcolithic? Those are the questions that are interesting and that will be answered eventually by aDNA. I’m not advocating anything in particular, just asking people interested in it to think about what seems to be the best explanation to get us to the IVC time with what we know.

    @raj, yes, literature may be clear, but I’m talking about preliterate societies. From Mesolithic to the Harappan period. And I’m not talking about language replacements or languages at all. Just about populations and their roles in Indian prehistory.

  13. Has anyone expanded on the relationship between Onge and Iran_Neo? IIRC, the authors of the South Asian paper modelled Onge as deriving 30% of its ancestry from an Iran_Neo population, but my guess would be that this is wrong. Could it be the other way around? Can Iran_Neo be modelled as Dzudzuana + Onge or something the like?

  15. About probable migration to India from outside before the Bronze Age, in Narasimhan et al. 2019, we read : ”Our finding, based on the sizes of blocks of ancestry (13) (fig. S59), that the mixture that formed the Indus Periphery Cline occurred by ~5400 to 3700 BCE—at least a millennium before the formation of the mature IVC—raises two possibilities. One is that Iranian farmer–related ancestry in this group was characteristic of the Indus Valley hunter-gatherers in the same way as it was characteristic of northern Caucasus and Iranian plateau hunter-gatherers. The presence of such ancestry in hunter-gatherers from Belt and Hotu Caves in northeastern Iran increases the plausibility that this ancestry could have existed in hunter-gatherers farther east. An alternative is that this ancestry reflects movement into South Asia from the Iranian plateau of people accompanying the eastward spread of wheat and barley agriculture and goat and sheep herding as early as the seventh millennium BCE and forming early farmer settlements, such as those at Mehrgarh in the hills flanking the Indus Valley (59, 60). However, this is in tension with the observation that the Indus Periphery Cline people had little if any Anatolian farmer–related ancestry, which is strongly correlated with the eastward spread of crop-based agriculture in our dataset.
    Thus, although our analysis supports the idea that eastward spread of Anatolian farmer–related ancestry was associated with the spread of farming to the Iranian plateau and Turan, our results do not support large-scale eastward movements of ancestry from western Asia into South Asia after ~6000 BCE (the time after which all ancient individuals from Iran in our data have substantial Anatolian farmer–related ancestry, in contrast to South Asians who have very little)…”
    https://scholar.harvard.edu/files/vagheesh/files/eaat7487.full_.pdf

    From the Neolithic Mehrgarh there is continuity for many aspects of course, but there is a change with the Chalcolithic Mehrgarh , a change involving also burials and anthropological features of the skeletons. After that, as remarked by Kennedy,there is not a significant anthropological change until Iron age Sarai Khola after 800 BCE, of course too late for the IAMT and not involving the whole of the subcontinent.

    Here some remarks from the book of Possehl ”The Indus Civilization: A Contemporary Perspective”:-
    https://books.google.co.in/books?id=pmAuAsi4ePIC&pg=PA175&lpg=PA175&dq=iron+age+sarai+khola+discontinuity&source=bl&ots=8A3gAT5yEY&sig=ACfU3U1iMwHUMD_I4fVESGobk93063PSGQ&hl=en&sa=X&ved=2ahUKEwj91Mm3gO_kAhXkILcAHbqJAp0Q6AEwA3oECAcQAQ#v=onepage&q=iron%20age%20sarai%20khola%20discontinuity&f=false
    And also from the book of Bryant and Patton ”The Indo-Aryan Controversy: Evidence and Inference in Indian History”: –
    https://books.google.co.in/books?id=fHYnGde4BS4C&pg=PA31&lpg=PA31&dq=iron+age+sarai+khola+discontinuity&source=bl&ots=qEYmMxjAH2&sig=ACfU3U3S6qJ6TIxJUL-hM3_InQDIxj7Jdg&hl=en&sa=X&ved=2ahUKEwj91Mm3gO_kAhXkILcAHbqJAp0Q6AEwBHoECAYQAQ#v=onepage&q=iron%20age%20sarai%20khola%20discontinuity&f=false

  16. @ alberto “At some point back in time, these two populations would have been exactly that, two different populations. Who lived where? Who were the first farmers and who the hunter-gatherers? Did the Neolithic bring migration from outside India? And the Chalcolithic?”

    Firstly, many thanks for this tool. Its easy to use for a newbie like me. What distance % is acceptable?

    Maybe i didnt put my view across properly or maybe the facts i presented were wrong, in which case kindly correct me.

    1. It would be fair to say, and most will agree, that the indus periphery samples (dated 3000-2000bce) were from between the area of western afghanistan and rakhigarhi.
    2. As per Narsimhan’s modeling, the swat valley IA (1000bce) samples (which fall in the above geographic area) all fall on the indus periphery and steppe_mlba cline, with need for no extra AHG ancestry. Pic of the cline modeled by Narsimhan that swat valley samples fall on (green bubbles) https://ibb.co/1dSmpBb. Correct me if im wrong in this analysis.
    3. So it would be fair to say that at least in the swat valley and surrounding regions, there was no hidden AASI rich population (ie. AASI>50pc) which admixed between 2500 & 1000bce. Thats a huge time gap. Again, correct me if Im wrong in this conclusion.
    4. So, if theres no AASI rich population in the swat region post 2500bce, its most likely that there was no AASI rich population there prior to 2500Bce as well. Unless they were present but culled or driven out to south east.

    This leads us to the conclusion that the swat area was never AASI rich prior to 2500bce, but was IranN rich. Reich sort of agrees when he states “We say ‘Iranian-related’ because we don’t know where they lived,” Reich says. They could have lived in the Iranian plateau, but the team’s data point to them having lived in South Asia for many thousands of years before the Indus Valley Civilisation, he adds.”

    More aDNA will be great, of course and will make the picture clearer.

  17. @Nirjhar

    Thanks, that’s what I understood from the scarce available data too. Mehrgarh seems to be the only site with anthropological data from the Neolilithic to the Chalcolithic, and some sort of discontinuity is found between both.

    It seems correct too that West Iran was getting Anatolian admixture since around 6000 BC (though Seh_Gabi_LN from c. 5700 BC still have very small amount, I think), so a Chalcolithic migration from that area doesn’t fit well with the Indus periphery samples. However, Chalcolithic Turan is still a fitting source for Indus periphery samples.

  18. @A

    I don’t think I need to correct you about what you’re saying. And I agree that the Swat Valley is very unlikely to have been a place with a AASI-rich population before 2000 BC. From all the possible places in historical India that one seems the least likely of all.

    But my question is different. I’m wondering about how the Indus Cline (if it gets confirmed with further sampling from the area in question) came to be. I thought this was an interesting question regarding the prehistory of South Asia, but maybe from a South Asian point of view it’s actually an uncomfortable one. On the other hand, I don’t think that if someone was uncomfortable with finding out about their prehistory they would be here in the first place. So I don’t know what to think.

  19. if people are curious about indian genetic history why dont you put your theories and questions to the authors of the recent papers at harvard or to niraj rai directly

    they seem eager to talk these days

  20. @alberto
    if your question is why there is variability in the indus periphery samples wrt iranN & AHG, my answer is that i dont know. Maybe it has to do with how western/eastern the location of admixture is. then again, it could be social standing. Also, i dont understand why the question would make someone uncomfortable.

    Modern indian pops prefer SiS_BA2(InPe with higher AHG) over lowest AHG InPe, except for Kalash. I also found that Kangju seems to be the best steppe source for Kashmiri Pandits, for other north indians not so much.

    -Central_Steppe_Emba at Kumsay & Mereke chooses Indus_periphery_0AHG as provided by Matt over Ganj_Dareh_N in all 6 samples, if this is even a valid test. Results
    https://ibb.co/LJnGFr5

  21. @a, when I use a lot more competing populations KAZ_Kumsay_EBA (which is like Mereke_EBA), tends to select Piedmont_Eneo (samples from Progress and Vonyuchka sites in the Caucasus which can used to model most of the ancestry of Yamnaya), with some Sarazm_EN, while KAZ_Dali_EBA tends to prefer Sarazm_Eneo, compared to the 0AHG zombie, but with some Piedmont_Eneo. The separate samples KAZ_EMBA prefer just being NE Asian+WSHG.

    I would guess each of these populations is a mix of Botai like WSHG like pops with different balances of the influences entering Kazakhstan at the time?

    (Graphic: https://imgur.com/a/HELwJiV – just done after the end of my other modelling upthread to see how Vahaduo behaves generally and if it replicates other fits well. It looks pretty good, but I’m not sure how it handles very distal modelling.).

    I guess it’s not implausible that if the hypothetical 0AHG population did exist, then it may have some ancestral relationship with Sarazm_EN, though.

  22. @A

    Ok, sorry, I probably got the impression from lumping together the answers from yourself and @raj, neither of which addressed the question but it seems for different reasons.

    The Kumsay_EBA samples are interesting, as they are contemporary with the earliest Yamnaya and Afanasievo. The only male is Q1a, and as Matt said above they’re mostly a mix of West Siberia/Kazakhstan hunter-gatherers and some Progress-like population. They’re too late for any sort of Iran_N admixture, so you’d need to include something like Geoksiur_En to get better models: https://ibb.co/r3tYH1Y

    Also to complement the models from the post with steppe admixture in post BMAC I run a non-exhaustive list of samples from the central steppe LBA (Sheet 1) and IA (Sheet 2):

    https://docs.google.com/spreadsheets/d/1_cBdRdk-F9wtPiM8RsZwPsFSKUVxc3CPKRwjeTJ2TuE/edit?usp=sharing

    Also rather patchy admixture from the south, though more significant in the LBA period especially (where steppe admixture in Turan is hardly showing up). Low levels of Indus periphery too all around.

  23. Hi Alberto

    Iran Neo like ancestry was almost certainly present in India in Mesolithic and even before.
    But I am pretty sure that there was another migration from West Asia to South Asia before IVC formed. Some haplotypes there are too young to be of Mesolithic origin.

  24. the rakhigarhi paper was pretty clear about the separation timeline and indicating it was out of india flow at various times

    people should just contact the authors if the paper was not clear enough

    the genetics data matches both archaeology and some of the linguistic out of india theories so all evidences line up

    the kowtow to steppe orthodoxy was likely unavoidable for publication in a western journal

    but just the mention of the phrase out of india broke the cone of silence and western walled garden of ignorance

    various attempts to resurrect anatolian and out of iran theories however contrived are to be expected since oit basically implies romans greeks persians etc were all punjabis once haha

  25. @Aram

    Yes, that’s what I think is most likely. Rather than an all or nothing, there’s probably a mix of both local West Eurasian and other coming from migration. We’ll have to see with ancient DNA the details.

  26. @matt @alberto i was only trying to distally model central steppe emba as vagheesh did with inputs as AnatoliaN, PPN, EEHG, WEHG, WSHG, ganj_darehN & 0AHG. only that i found it pulling towards 0AHG and not Ganj_dareh.

    I agree that for proximal modeling the best sources would be different and you guys have analyzed that above.

    My question to Matt & Alberto is this – is the tool good enough to differentiate between Ganj_dareh_N & 0AHG, or are the 2 so close and the inut data so crude that the results are useless?
    For eg Parkhai_En is modeled by the vahaduo tool distally as 50% 0AHG, 42% Ganj_Dareh_N, rest Anatolia_N with a distance of 3.4%. Removing either of 0AHG or Ganj_Dareh worsens distance to 4.5+%. Can we conclude that Parkhai EN contains both of these cousin ancestries?

    Another issue could be that Ganj_Dareh is older whereas 0AHG is simulated from a 3000bce sample. How does it affect the comparison between ganj_dareh_N & 0AHG especially when targets are closer to 3000bce and 8000bce respectively?

    Matt said “if the hypothetical 0AHG population did exist”
    it was my uderstanding that such a population did exist as per Shinde2019. The only question was where and at what time. Did I read it wrong?

  27. @A

    Yes, the tool is good enough to differentiate Ganj_Dareh-N and 0AHG simulation, since they are not too similar to each other. Ganj_Dareh_N is what I called in the post “West Iranian”, while the 0AHG simulation is closer to “East Iranian” (close to Shahr-i-Sokhta_BA1 samples and to the Eneolithic samples from Turan). Adding it as the target and using the whole Global 25 datasheet with individuals as sources, here’s the top 25 closest ones to it.

    https://ibb.co/tJgKqLw

    All the samples between West Iran and Eastern Central Asia are a mix of Iran_N and something like Sarazm_En. There was probably a cline since the Mesolithic, but movements continued all the time, with later arrival of Anatolian ancestry too.

    So both Parkhai_En and the 0AHG simulation can be modelled as a mix of those ancestries. 0AHG can only represent one individual, not so much a population from that time, since we’ve seen that there is enough variability between samples. So I guess that populations with individuals very similar to 0AHG indeed existed over a very broad area of Iran, SC Asia and maybe North India.

    Proximate sources are usually favoured in modelling, but sometimes older ones are picked up too if they are needed for a better model, so there is no rule about the time of the samples.

  29. talageri danino kazanas and some others all have their own models

    basically some version of people left west and north west

    i have posted papers possibly dating some of this to circa 4500 BC to 2200 BC anatolia caucasus caspian etc

    but it really is european history not ours so it is upto europeans to figure out the details not indians

    as long that doesnt involve denying indian history denigrating hindus taking credit for sanskrit or playing divisive indian politics it is not any of indian business and we can go our own ways

  30. “So both Parkhai_En and the 0AHG simulation can be modelled as a mix of those ancestries. 0AHG can only represent one individual, not so much a population from that time, since we’ve seen that there is enough variability between samples. So I guess that populations with individuals very similar to 0AHG indeed existed over a very broad area of Iran, SC Asia and maybe North India.”

    Yes, this west-iranian to east-iranian cline is quite clear, from Tepe-Hissar to Parkhai to Namazga to Sarazm.

  31. https://ibb.co/jrQtTgk

    Modern North Indian pops do like Kangju more than Sintashta for steppe. Kokcha & kashkarchi are rejected.

    Only Kashmiri Pandits only settle for Kangju/Kushana as steppe source. This makes sense as Kushanas ruled Kashmir for over 2 centuries.

    So it seems likely that steppe entered india in at least 2 waves. The 2nd wave was in historical period.

  32. @A: it was my uderstanding that such a population did exist as per Shinde2019. The only question was where and at what time. Did I read it wrong?

    As I understand it, the thing with hypothetical populations is like, take a scenario like: you have populations A, B, C. They mix to create AC and BC, which then drift and then mix with each other ABC and drift more. But if you tried to extract C from ABC, you’d end up with a population AB that actually never existed historically!

    It’s that kind of thing – you may be able to extract an AB (0 AHG) by removing C (100 AHG), but such a population may never have existed historically without C.

    I think Alberto has answered on the point about Iran_N vs 0AHG.

  33. “It’s that kind of thing – you may be able to extract an AB (0 AHG) by removing C (100 AHG), but such a population may never have existed historically without C.”

    Thanks for the explanation. This is a problem only if there are 3 populations? What if there are only 2 separate populations A & C (0AHG & 100AHG, a 3rd population is not being expected). The above conundrum does not apply in this case? If C is removed, you should be left with A which has to exist in reality?

  34. @A

    Obviously if you have a population which is a mix of two other ones, then those two other ones must have existed. So under this assumption, as you said before, the question is where and when. Which ends up being the same question I was asking from the beginning.

  35. what difference does it make to europeans turan or punjab

    zagros caucasus are borderlands turan was crossroad of civilizations not a center of anything let alone high culture robust social ordering or technological innovations

    why seek genesis amongst the barbarian hordes its really a puzzle

  36. ”why seek genesis amongst the barbarian hordes its really a puzzle”
    We don’t exactly get the impression of ”barbarian hordes” when we study Vedas, Avesta, Iliad etc do we? 🙂 , those emerged when life was more or less settled & there was a civilization .

  37. @matt
    Is kangju being selected for modern pops due to the high steppe component (>60%)?
    Narsimhan theorized that ANI was such a population (with 53% steppe_mlba on the steppe Cline). So he thinks there’s such a ghost pop prior to swat valley IA which gave rise to modern indians.

    Also Im surprised as to how Kangju could not be rejected by Narsimhan, but Kushan did. Both Kangju and Kushan seem to have a similar Han component.

  39. @raj, i don’t think anyone is denying presence of civilization/settled life in india/south asia prior to the supposed steppe migration.

  40. the r1a paper supposedly claims himalayan roots and possibly out of india migration to the steppes

    so this could be archaeologically distinctive evidence in support

  41. “the r1a paper supposedly claims himalayan roots and possibly out of india migration to the steppes” — @Raj, I saw the slides from the upcoming paper in Dr Chaubey’s presentation. When do you think this migration occured ? We already have some AASI/AHG related ancestry in samples dating ~2500 BCE in North india and eastern iran.

  42. sometime before corded ware appeared on the steppes and europe with r1a and the autosome

    and the doggie haha

  43. @ Raj

    How does an IE homeland in EE denigrate Indians ? Sanskrit was obviously invented somewhere down that way
    If you propose an OIT homeland, then we need to account for all Phyla; not just Indo-Aryan. I’m open to scenarios .

  44. i meant denigrating hindus with all the labelling and spurious dating of our history

    there is nothing obvious about the invention of sanskrit and lot of debate about the various dates

    talageri and others have some models maybe right or wrong and anyway not relevant to the indian big picture since it is for europeans

    btw lets see the hindu number system referred as such in the west

    or do you call iphones as apple fedex iphones

  45. and if people check the phoenician dna paper closely the winds of change are blowing for the origin of your alphabets as well

    lots of fireworks in the decades to come

    or maybe the same old same old lets see

  46. “talageri and others have some models maybe right or wrong and anyway not relevant to the indian big picture since it is for europeans” —- @Raj, How do you explain the varying Steppe_MLBA related ancestry in modern south asians(varying along geographical and jaati cline) ?

    “How does an IE homeland in EE denigrate Indians ?” — I don’t think it matters for most indians 🙂 , however, raj might be scared that it might aggravate existing faultlines.

  47. steppe mlba doesnt matter if r1a itself is out of india

    seems to be have been mostly women anyway and i dont judge peoples marital preferences haha

    as explained it is not the ie homeland issue per se but the denigration of hindus who talk about oit and getting labelled xyz to shut down the debate

    i dont mind faultlines and hope such lines are well respected

  48. “seems to be have been mostly women anyway and i dont judge peoples marital preferences haha” —@Raj, that seems to be the case with swat valley aDNAs, however, interior india’s modern day samples show the opposite pattern.

  49. @raj

    If you have been following this blog fo some time you probably know that no one here is against anything that’s well argued and based on facts. This blog is about West Eurasian history, and not about politics. You won’t see here debates of whether the people living in the Eurasian steppe in the EMBA were European or not, because there’s not point in back projecting modern political entities into deep prehistory.

    So I hope that you can understand that your comments, the tone in them and the content, are out of place here. There are many places out there were you will find people willing to have some fight about those political topics, but not here.

    If you want to contribute respectfully to any topic being debated you’re welcome, and you can post some interesting paper that we (many of us) might not know, like the one about corded incised pottery above (interesting paper, though it’s about the possible interactions between East India and SE Asia and possibly China, and not relevant for the rest of West Eurasia as far as I can tell from my quick glance at it now).

    I welcome a speculative, but realistic enough, scenario about an out of India hypothesis if you want to elaborate. But you’ll have to deal with the questions I opened in the post in order to do that, because you’d need an out of India migration of a population that should be 100% West Eurasian (East Iranian, basically), so that should predate the admixture with an AASI-rich population that we already see in the Harappan period. And you’d need to explain why such AASI-rich population living beyond the Vindhyas (at a time when they would still be hunter-gatherers) decided to cross it and enter the urban centres in the NW part of India and had such a significant genetic impact in that urban BA population.

    If you are willing to participate here in such way (without negative attitudes against anyone, with respectful and informative comments that may provide interesting alternative views) you’re welcome. You will be received with respectful and helpful feedback, even when in disagreement.

  50. Re. Chaubey’s presentation, I’m waiting to see the paper. If the conclusions came from some amateur I would not give them a second thought, but Gyaneshwer Chaubey is a well respected scientist and has been working for many years in that field.

    From one of the slides, I kind of understood that what he proposes is that the split between R1a-Z2123 and R1a-L657 is quite older (some 2000 years) than previously estimated. But we’ll need to wait for the paper to really see what are the findings.

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