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Saturday, May 19, 2018

Global25 PAST-compatible datasheets

I'm planning to run regular workshops over the next few months on how to get the most out of Global25 data with various programs, and expecially PAST (see here). So if you have Global25 coordinates, please stay tuned.

To that end, I've put together four color-coded, PAST-compatible Global25 datasheets with thousands of present-day and ancient samples, available at the links below:





PAST is an awesome little statistical program and simple to use. The manual is available here. To kick things off, here's a quick guide how to run a Neighbor Joining tree on your Global25 coordinates:

- download the Global_25_PCA_pop_averages_scaled.dat from the last link above

- open the dat file with something a little more advanced than Windows notepad, like, say, TextPad (see here)

- stick your scaled coordinates at the bottom of the sheet, so that they look exactly like those of the other samples, except give yourself an original symbol, like, say, a black star

- open the edited dat file with PAST and choose all of the columns and rows by clicking the empty tab above the labels

- then, at the top, go to Multivariate > Clustering > Neighbor joining

After a few seconds you should see a nice, color-coded tree like the one below, except you'll also be on it, in black text. I'm very happy with these results, by the way. As far as I can see, all of the populations and individuals cluster exactly where they should.

Those of you who are already very proficient in using PAST, feel free to go nuts with these new datasheets and show us the results in the comments below. I'll try to put together a workshop for beginners within the next couple of weeks.

See also...

Modeling genetic ancestry with Davidski: step by step

Wednesday, May 16, 2018

On the genetic prehistory of the Greater Caucasus (Wang et al. 2018 preprint)

Finally, the focus shifts to the Eneolithic/Bronze Age North Caucasus. In a new manuscript at bioRxiv, Wang et al. present genome-wide SNP data for 45 prehistoric individuals from the region along a 3000-year temporal transect (see here). From the preprint (emphasis is mine):

Based on PCA and ADMIXTURE plots we observe two distinct genetic clusters: one cluster falls with previously published ancient individuals from the West Eurasian steppe (hence termed ‘Steppe’), and the second clusters with present-day southern Caucasian populations and ancient Bronze Age individuals from today’s Armenia (henceforth called ‘Caucasus’), while a few individuals take on intermediate positions between the two. The stark distinction seen in our temporal transect is also visible in the Y-chromosome haplogroup distribution, with R1/R1b1 and Q1a2 types in the Steppe and L, J, and G2 types in the Caucasus cluster (Fig. 3A, Supplementary Data 1). In contrast, the mitochondrial haplogroup distribution is more diverse and almost identical in both groups (Fig. 3B, Supplementary Data 1).

Thus, the most important "Indo-European" Y-haplogroups today, R1a-M417 and R1b-M269, did not arrive in Europe from the Caucasus or Near East. They're native to Europe. Hence, it appears that Eneolithic/Bronze Age Eastern Europeans mostly acquired their Near Eastern-related ancestry via female exogamy from populations in the Caucasus. That's basically what I've been arguing for a few years now. It feels good to be vindicated, especially considering the unfair criticism that I was subjected to here and elsewhere because of expressing this opinion (for instance, see here).

However, as far as I can see, based on the samples in this preprint, neither the Caucasus Maykop nor steppe Maykop appear to be unambiguous sources of this southern admixture in ancient Eastern Europe. That's because the Caucasus Maykop mtDNA profile still looks somewhat off in this context, while steppe Maykop harbors West Siberian forager-related genome-wide ancestry that is practically absent in the Yamnaya and all other closely related peoples.

In any case, please note the happy coincidence that academia has finally caught up to this blog and managed to find European farmer-derived ancestry in Yamnaya:

Importantly, our results show a subtle contribution of both Anatolian farmer-related ancestry and WHG-related ancestry (Fig.4; Supplementary Tables 13 and 14), which was likely contributed through Middle and Late Neolithic farming groups from adjacent regions in the West. A direct source of Anatolian farmer-related ancestry can be ruled out (Supplementary Table 15). At present, due to the limits of our resolution, we cannot identify a single best source population. However, geographically proximal and contemporaneous groups such as Globular Amphora and Eneolithic groups from the Black Sea area (Ukraine and Bulgaria), which represent all four distal sources (CHG, EHG, WHG, and Anatolian_Neolithic) are among the best supported candidates (Fig. 4; Supplementary Tables 13,14 and 15).

Check out what I had to say about this issue exactly two years ago: Yamnaya = Khvalynsk + extra CHG + maybe something else. Not bragging, just making a point that I do know what I'm doing here, most of the time anyway.

Wang et al. conclude their preprint with, unfortunately I have to say, some downright bizarre comments in regards to the Proto-Indo-European (PIE) homeland debate. But I'll get back to that later, when the ancient data from this and forthcoming related papers are released online.


Wang et al., The genetic prehistory of the Greater Caucasus, bioRxiv, posted May 16, 2018, doi:

See also...

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

New PCA featuring Botai horse tamers, Hun and Saka warriors, and many more...

Just in case anyone's wondering how the ancient samples from the two recent archaeogenetic papers by Damagaard et al. (Nauture and Science) behave in my two main Principal Component Analyses (PCA), here you go:

The relevant datasheet is available here. Over 90 of the new samples made into onto this plot, but to keep things simple I only highlighted a few of them. To see the positions of any or all of the rest, plug the datasheet into, say, PAST (freely available here) and create your own version of the plot. Also, below are links to updated Global25 datasheets, featuring coordinates for almost all of the new samples (available separately here).

Global 25 datasheet

Global 25 datasheet (scaled)

Global 25 pop averages

Global 25 pop averages (scaled)

The interesting thing about those Tien Shan nomads, especially the Kangju people, is that they're much more West Eurasian (European + West Asian) than the Asian Scythians sampled to date. However, despite this, they're still no good for modeling the West Eurasian ancestry of most South Asian populations. I've looked at this closely, and the Steppe_MLBA cluster is still the one to beat in this respect.

See also...

Genetic ancestry online store (to be updated regularly)

Sunday, May 13, 2018

Hittite-era Anatolians in qpAdm

The apparent lack of steppe ancestry in five Hittite-era, perhaps Indo-European-speaking, Anatolians was interpreted in Damagaard et al. 2018 as a major discovery with profound implications for the origin of the Anatolian branch of Indo-European languages.

But I disagree with this assessment, simply because none of these Hittite-era individuals are from royal Hittite, or Nes, burials. Hence, there's a very good chance that they were Hattians, who were not of Indo-European origin, even if they spoke the Indo-European Hittite language because it was imposed on them.

Moreover, I am actually seeing a minor, but persistent, signal of steppe ancestry in one of the two Old-Hittite Period (~1750–1500 BCE) samples: Anatolia_MLBA MA2203. Indeed, I can put together very coherent, chronologically sound models using a couple of different methods to demonstrate this. Below is a fairly decent qpAdm model.

Anatolia_EBA 0.794±0.073
Ukraine_Eneolithic_I6561 0.206±0.073
tail: 0.400704
Full output

Obviously, these numbers aren't exactly impressive. But if the signal is real, then it might be an indication of things to come when someone manages to sequence at least a few genomes from confirmed Hittite remains. None of the other Anatolia_MLBA individuals, three of whom are from the Assyrian Colony Period (~2000–1750 BCE), show such obvious steppe ancestry.

Anatolia_EBA 1.000
Ukraine_Eneolithic_I6561 0.000
tail: 0.449485
Full output

Anatolia_EBA 0.983±0.069
Ukraine_Eneolithic_I6561 0.017±0.069
tail: 0.618499
Full output

Anatolia_EBA 0.868±0.089
Ukraine_Eneolithic_I6561 0.132±0.089
tail: 0.708811
Full output

Anatolia_MLBA w/o MA2203
Anatolia_EBA 1.000
Ukraine_Eneolithic_I6561 0.000
tail: 0.286377
Full output

In any case, apart from all of that, Damagaard et al. do take a measured and sober approach to interpreting their archaeogenetic data in the context of the Indo-European homeland debate. The paper also includes a very thorough linguistic supplement, freely available here, which reveals that there is Eastern European Hunter-Gatherer (EHG) ancestry in soon to be published Maykop culture samples. From the supplement (emphasis is mine):

Despite a general agreement on a Pontic-Caspian origin of the Anatolian Indo-European language family, it is currently impossible to determine on linguistic grounds whether the language reached Anatolia through the Balkans in the West (Anthony 2007; Mallory 1989: 30; Melchert 2003; Steiner 1990; Watkins 2006: 50) or through the Caucasus in the East (Kristiansen 2005: 77; Stefanini 2002; Winn 1981). From their earliest attestations, the Anatolian languages are clustered in Anatolia, and if the distribution reflects a prehistoric linguistic speciation event (as argued by Oettinger 2002: 52), then it may be taken as an indication that the arrival and disintegration of Proto-Anatolian language took place in the same area (Steiner 1981: 169). However, others have reasoned that the estimated period between the dissolution of the Proto-Anatolian language and the attestation of the individual daughter languages is extensive enough to allow for prehistoric mobility within Anatolia, theoretically leaving plenty of time for secondary East-to-West dispersals (cf. Melchert 2003: 25).

Whatever the case may be, there are no linguistic indications for any mass migration of steppe-derived Anatolian speakers dominating or replacing local populations. Rather, the Anatolian Indo-European languages appear in history as an organically integrated part of the linguistic landscape. In lexicon, syntax, and phonology, the second millennium languages of Anatolia formed a convergent, diffusional linguistic area (Watkins 2001: 54). Though the presence of an Indo-European language itself demonstrates that a certain number of speakers must have entered the area, the establishment of the Anatolian Indo-European branch in Anatolia is likely to have happened through a long-term process of infiltration and acculturalization rather than through mass immigration or elite dominance (Melchert 2003: 25). Furthermore, the genetic results presented in Damgaard et al. 2018 show no indication of a large-scale intrusion of a steppe population. The EHG ancestry detected in individuals associated with both Yamnaya (3000–2400 BCE) and the Maykop culture (3700–3000 BCE) (in prep.) is absent from our Anatolian specimens, suggesting that neither archaeological horizon constitutes a suitable candidate for a “homeland” or “stepping stone” for the origin or spread of Anatolian Indo-European speakers to Anatolia. However, with the archaeological and genetic data presented here, we cannot reject a continuous small-scale influx of mixed groups from the direction of the Caucasus during the Chalcolithic period of the 4th millennium BCE.


Under the “Steppe Hypothesis,” the Indo-Iranian languages are not seen as indigenous to South Asia but rather as an intrusive branch from the northern steppe zone (cf. Anthony 2007: 408–411; Mallory 1989: 35–56; Parpola 1995; Witzel 1999, 2001). Important clues to the original location and dispersal of the Indo-Iranians into South and Southwest Asia are provided by the Indo-Iranian languages themselves.

The Indo-Aryan and Iranian languages share a common set of etymologically related terms related to equestrianism and chariotry (Malandra 1991). Since it can be shown that this terminology was inherited from their Proto-Indo-Iranian ancestor, rather than independently borrowed from a third language, the split of this ancestor into Indo-Aryan and Iranian languages must postdate these technological innovations. The earliest available archaeological evidence of two-wheeled chariots is dated to approximately 2000 BCE (Anthony 1995; Anthony and Ringe 2015; Kuznetsov 2006: 638–645; Teufer 2012: 282). This offers the earliest possible date so far for the end of Proto-Indo-Iranian as a linguistic unity. The reference to a mariannu in a text from Tell speakers. Leilān in Syria discussed below pushes the latest possible period of Indo-Iranian linguistic unity to the 18th century BCE.


The traces of early Indo-Aryan speakers in Northern Syria positions the oldest Indo-Iranian speakers somewhere between Western Asia and the Greater Punjab, where the earliest Vedic text is thought to have been composed during the Late Bronze Age (cf. Witzel 1999: 3). In addition, a northern connection is suggested by contacts between the Indo-Iranian and the Finno-Ugric languages. Speakers of the Finno-Ugric family, whose antecedent is commonly sought in the vicinity of the Ural Mountains, followed an east-to-west trajectory through the forest zone north and directly adjacent to the steppes, producing languages across to the Baltic Sea. In the languages that split off along this trajectory, loanwords from various stages in the development of the Indo-Iranian languages can be distinguished: 1) Pre-Proto-Indo-Iranian (Proto-Finno-Ugric *kekrä (cycle), *kesträ (spindle), and *-teksä (ten) are borrowed from early preforms of Sanskrit cakrá- (wheel, cycle), cattra- (spindle), and daśa- (10); Koivulehto 2001), 2) Proto-Indo-Iranian (Proto-Finno-Ugric *śata (one hundred) is borrowed from a form close to Sanskrit śatám (one hundred), 3) Pre-Proto-Indo-Aryan (Proto-Finno-Ugric *ora (awl), *reśmä (rope), and *ant- (young grass) are borrowed from preforms of Sanskrit ā́ r ā- (awl), raśmí- (rein), and ándhas- (grass); Koivulehto 2001: 250; Lubotsky 2001: 308), and 4) loanwords from later stages of Iranian (Koivulehto 2001; Korenchy 1972). The period of prehistoric language contact with Finno-Ugric thus covers the entire evolution of Pre-Proto-Indo-Iranian into Proto-Indo-Iranian, as well as the dissolution of the latter into Proto-Indo-Aryan and Proto-Iranian. As such, it situates the prehistoric location of the Indo-Iranian branch around the southern Urals (Kuz’mina 2001).


Guus Kroonen, Gojko Barjamovic, & Michaël Peyrot. (2018). Linguistic supplement to Damgaard et al. 2018: Early Indo-European languages, Anatolian, Tocharian and Indo-Iranian.

Update 14/05/2018: I managed to, more or less, reproduce my qpAdm models with qpGraph. This is never a simple and easy task, so I'm now more confident that Anatolia_MLBA MA2203 really does harbor ancestry from the steppe.

See also...

Likely Yamnaya incursion(s) into Northwestern Iran

Graeco-Aryan parallels

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Thursday, May 10, 2018

Graeco-Aryan parallels

The clearly non-local admixture in the geographically and genetically disparate, but Indo-European-speaking, ancient Mycenaeans and present-day North Indian Brahmins is very similar. So similar, in fact, that it could derive from practically the same population in space and time. The most plausible source for this admixture are the Bronze Age herders of the Pontic-Caspian steppe and their immediate descendants, such as those belonging to the Sintashta, Srubnaya, and other closely related archaeological cultures.

To prove and simultaneously illustrate this point, below are a couple of Admixture graph or qpGraph analyses. Note that I was also able to add Balkans_BA I2163 to the Mycenaean model. This is an Srubnaya-like ancient sample from the southern Balkans dating to the early Mycenaean period. Not only does Balkans_BA I2163 help to further constrain the model, but it also suggests a proximate source of steppe-related admixture into the population that potentially gave rise to the Mycenaeans. The relevant graph files are available here.

Considering that the Bronze Age peoples of the Pontic-Caspian steppe are the only obvious and direct, and, hence, most plausible link between the Mycenaeans and Brahmins, it follows that they are also the most likely vector for the spread of Indo-European speech to ancient Greece and South Asia. Or not? But if not, then what are the alternatives, and I mean real alternatives, not just excuses? If you think that you can offer a genuine alternative then feel free to do so in the comments below. However, be warned, stupid sh*t won't be tolerated.

See also...

Main candidates for the precursors of the proto-Greeks in the ancient DNA record to date

On the doorstep of India

Steppe admixture in Mycenaeans, lots of Caucasus admixture already in Minoans (Lazaridis et al. 2017)

Monday, May 7, 2018

Protohistoric Swat Valley peoples in qpGraph #2

Three options. Just one passes muster; the one with Sintashta. Coincidence? I think not. Who still wants to claim that there's no Sintashta-related steppe stuff in these Iron Age SPGT South Asians? The relevant graph files are available here. Any ideas for better models?

Update 08/05/2018: The reason that I chose Dzharkutan1_BA, from what is now Uzbekistan, as the BMAC proxy in the above graphs was because it's geographically a proximate choice for SPGT. However, I've since discovered that Gonur1_BA, from what is now Turkmenistan, does a somewhat better job in these models. The additional graph files are available at the same link as above here.

See also...

Protohistoric Swat Valley peoples in qpGraph

The protohistoric Swat Valley "Indo-Aryans" might not be exactly what we think they are

Friday, May 4, 2018

The protohistoric Swat Valley "Indo-Aryans" might not be exactly what we think they are

I need some help interpreting these linear models of ancient and present-day South Asian populations. Overall, the Iron Age groups from the Swat Valley, or SPGT, look like rather obvious outliers. The relevant datasheet is available here.

This might be because of significant bidirectional gene flow and/or continuity between Central Asia and the northern parts of South Asia before Sintashta-related steppe herders showed up in the region, and even before the Bactria Margiana Archaeological Complex (BMAC) got going. Note that Dzharkutan1_BA is an BMAC sub-population from near South Asia, but it doesn't quite have the same effect on those Swat Valley samples as the pre-BMAC Shahr_I_Sokhta_BA1 from the present-day Iranian/Afghan border.

If true, it probably means that most of the Iron Age peoples of the Swat Valley shouldn't be modeled as simply a mixture of Indus_Periphery and Steppe_MLBA. That's because they appear to be in part of the same or similar type of ancestry as Shahr_I_Sokhta_BA1. And indeed, qpAdm also suggests that they are.

Indus_Periphery 0.692±0.042
Shahr_I_Sokhta_BA1 0.104±0.045
Sintashta_MLBA 0.204±0.015
Tail: 0.659609
Full output

I'm trying to incorporate this new information into my Admixture graph models of the SPGT groups (see here). If I manage to come up with something useful I'll update this post with the results.

Update 08/05/2018: see here.

Wednesday, May 2, 2018

Open analysis thread: genetic distance (Fst) matrix focusing on ancient Central and South Asia

I'm hoping that we can learn something new about the genomic prehistory of Eurasia, and especially Central and South Asia, based on this massive new Fst matrix:

Ancient Central and South Asia genetic distance (Fst) matrix

Hint: it's probably easiest to initially explore this format with a program called PAST. Indeed, if you'd like to model fine scale ancestry proportions based on these data, it might be a good idea to use PAST to first turn the matrix into a principal coordinates (PCoA) datasheet (like this).

On a related note, as I was typing this, commentator Chetan alerted me to a post at the Molgen forum claiming that Y-haplogroup R1b-L51 has turned up in Eneolithic remains from Pontic-Caspian steppe (see here). If true, then it's a big deal, because it's the best evidence yet that L51 expanded into Central and Western Europe from the steppes. This is the Google translation of the post. Emphasis is mine.

Hello. Today, the XIV Samara Archeological Conference was held. The following reports were heard. Khokhlov AA Preliminary results of anthropological and genetic studies of materials of the Volga-Ural region of the Neolithic-Early Bronze Age by an international group of scientists. In his report, AA Khokhlov. introduced into scientific circulation until the unpublished data of the new Eneolithic burial ground Ekatirinovsky cape, which combines both the Mariupol and Khvalyn features, and refers to the fourth quarter of the V millennium BC. All samples analyzed had a uraloid anthropological type, the chromosome of all the samples belonged to the haplogroup R1b1a2 (R-P 312 / S 116), and the haplogroup R1b1a1a2a1a1c2b2b1a2. Mito to haplogroups U2, U4, U5. In the Khvalyn burial grounds (1 half of the 4th millennium BC), the anthropological material differs in a greater variety. In addition to the uraloid substratum, European broad-leaved and southern-European variants are recorded. To the game haplogroup R1a1, O1a1, I2a2 are added to mito T2a1b, H2a1.

I'd say that this information sounds legit. But let's wait and see if the results are backed up by one of the major ancient DNA labs in the west, like the Reich Lab.

See also...

Late PIE ground zero now obvious; location of PIE homeland still uncertain, but...

Monday, April 30, 2018

Zoroastrian genetic origins revisited

About a year ago I found that the ancestry of present-day Iranians was best explained as largely a mixture between early Anatolian and Iranian farmers and Sarmatians from the Pontic-Caspian steppe (see here).

Things have now changed somewhat after the release of several hundred ancient samples from across Eurasia. Below are the best qpAdm models that I was able to find for various Iranian ethnic/regional populations based on my new dataset.

Ganj_Dareh_N 0.363±0.031
Hajji_Firuz_ChL 0.481±0.029
Karagash_MLBA 0.156±0.019
tail: 0.753635
Full output

Ganj_Dareh_N 0.056±0.042
Hajji_Firuz_ChL 0.883±0.039
Karagash_MLBA 0.061±0.027
tail: 0.862141
Full output

Ganj_Dareh_N 0.598±0.048
Hajji_Firuz_ChL 0.244±0.045
Karagash_MLBA 0.158±0.030
tail: 0.604908
Full output

Dashti_Kozy_BA 0.143±0.025
Ganj_Dareh_N 0.286±0.034
Hajji_Firuz_ChL 0.571±0.029
tail: 0.994129
Full output

Ganj_Dareh_N 0.309±0.035
Hajji_Firuz_ChL 0.556±0.029
Yamnaya_Samara 0.134±0.019
tail: 0.383344
Full output

Ganj_Dareh_N 0.279±0.045
Hajji_Firuz_ChL 0.600±0.048
Yamnaya_Samara 0.073±0.048
West_Siberia_N 0.048±0.033
tail: 0.413456
Full output

Ganj_Dareh_N 0.417±0.033
Hajji_Firuz_ChL 0.464±0.031
Karagash_MLBA 0.120±0.020
tail: 0.777933
Full output

Bustan_BA 0.352±0.053
Dashti_Kozy_BA 0.168±0.031
Hajji_Firuz_ChL 0.480±0.036
tail: 0.921955
Full output

However, all of the Iranian groups are still scoring a fair amount of ancient steppe ancestry, with the Zoroastrians ahead of the rest, which is potentially important, because they're basically a population relict from pre-Islamic Persia. Hence, this might be betraying their stronger ties to pre-Turkic, early Indo-Iranian Central Asia relative to the other Iranians. Also worth noting:

- As far as I can see, the Zoroastrians are the only Iranians in this analysis that really benefit from the addition of an Bactria Margiana Archaeological Complex (BMAC) reference population to their model, which might also be important, for the same reason outlined above

- There's no point modeling most of the Iranian groups as partly of Western Siberian forager (West_Siberia_N) origin, except perhaps the Mazandarani Iranians

- Indeed, Mazandarani Iranians are also the only group better modeled as part Yamnaya rather than Steppe_MLBA, which might be explained by Yamnaya-related incursions into what is now Northwestern Iran during the Early Bronze Age (see here)

- No matter what, I can't find a working model (P-value >0.05) for the Bandari Iranians using the new set of right pops aka outgroups, probably because the Bandaris harbor recent admixture from outside of Iran, including from Africa

On a related note, there's yet another feature in the Indian media about the impending publication of ancient DNA from the Harappan burial site at Rakhigarhi (see here). I've lost count of how many articles like this I've read over the last few years. But unlike the rest, this one actually reveals some specific information about the results: no Y-haplogroup R1a and no steppe ancestry in the Harappan sample or samples. So this time, I'd say that we're only days or weeks away from the publication of the relevant paper.

My final prediction in this context is that we'll see an ancient genome, or, hopefully, genomes, basically identical to the Indus_Periphery samples from Narasimhan et al. 2018 (see here). And then, apart from a few crazy people still shouting online that we need many more Harappan genomes because almost anything is yet possible, it'll be game over.

See also...

The mystery of the Sintashta people

On the doorstep of India

Indian smoke and mirrors

Friday, April 27, 2018

The mystery of the Sintashta people

During the Middle to Late Bronze Age, the steppes southeast of the Ural Mountains, in what is now Russia, were home to communities of metallurgists who buried their warriors with horses and the earliest examples of the spoked-wheel battle chariot.

We don't know what they called themselves, because they didn't leave any written texts, but their archaeological culture is commonly known as Sintashta. It was named after a river near one of their main settlements; an elaborate fortified town that has also been described as an ancient metallurgical industrial center. Another of their well known settlements, very similar to Sintashta, is Arkaim, pictured below courtesy of Wikipedia.

Sintashta is arguably one of the coolest ancient cultures ever discovered by archaeologists. It's also generally accepted to be the Proto-Indo-Iranian culture, and thus linguistically ancestral to a myriad of present-day peoples of Asia, including Indo-Aryans and Persians. No wonder then, that its origin, and that of its population, have been hotly debated issues.

The leading hypothesis based on archaeological data is that Sintashta is largely derived from the more westerly and warlike Abashevo culture, which occupied much of the forest steppe north of the Black and Caspian Seas. In turn, Abashevo is usually described as an eastern offshoot of the Late Neolithic Corded Ware Culture (CWC), which is generally seen as the first Indo-European archaeological culture in Northern Europe (see here).

Below is a Principal Component Analysis (PCA) featuring 38 Sintashta individuals from the recent Narasimhan et al. 2018 preprint. Note that the main Sintashta cluster overlaps almost perfectly with the main CWC cluster. The relevant datasheet is available here.

Moreover, many ancient and present-day South and Central Asians, particularly those identified with or speaking Indo-Iranian languages, appear to be strongly attracted to the main Sintashta cluster, forming an almost perfect cline between this cluster and the likely Indus Valley diaspora individuals who show no evidence of steppe ancestry.

This is in line with mixture models based on formal statistics showing significant Sintashta-related ancestry in Indo-Iranian-speakers (for instance, see here), and high frequencies of Y-haplogroup R1a-Z93 in both the Sintashta and many Indo-Iranian-speaking populations.

Some of the Sintashta samples are outliers from the main Sintashta cluster, and that's because they harbor elevated levels of ancestry related to the Mesolithic and Neolithic foragers of Eastern Europe and/or Western Siberia. This is especially true of a pair of individuals who belong to Y-haplogroup Q. However, this doesn't contradict archaeological data, which suggest that the Sintashta community may have been multi-cultural and multi-lingual. Indeed, it's generally accepted based on historical linguistics data that there were fairly intense contacts in North Eurasia between the speakers of Proto-Indo-Iranian, Proto-Uralic and Yeniseian languages.

Thus, it appears that there's not much left to debate because ancient DNA has seemingly backed up the most widely accepted hypotheses about the origin of Sintashta and its people, and their identification mainly as Proto-Indo-Iranian-speakers.

However, a sample from a Sredny Stog II culture burial on the North Pontic steppe, in what is now eastern Ukraine, has complicated matters somewhat. This individual, known as Ukraine_Eneolithic I6561, not only clusters very strongly with the most typical Sintashta samples, but also belongs to Y-haplogroup R1a-Z93. On the other hand, none of the CWC remains sequenced to date belong to this particular subclade of R1a (although, obviously, they do belong to a host of near and far related R1a subclades).

I've never seen anyone worth reading propose that Sintashta might derive from Sredny Stog II instead of Abashevo. And no wonder, because Sredny Stog II was long gone when Sintashta appeared in the archaeological record.

However, if CWC remains continue to fail to produce R1a-Z93, while, at the same time, the steppes of eastern Ukraine and surrounds are shown to be a hotbed of R1a-Z93 from the Sredny Stog to the Sintashta periods, which I think is possible, then ancient DNA might well force a serious re-examination of how the awesome Sintashta culture and people came to be.

See also...

On the doorstep of India

The beast among Y-haplogroups