Blast from the past: Yamnaya prediction from 2016

I wonder what's holding up the publication of the Wang et al. "Greater Caucasus" preprint? It was released back in May at the bioRxiv (see here). On a related note, I was looking back at some of the stuff that I wrote about the origin of the Yamnaya people (aka Steppe_EMBA), and found this...

But here's my prediction: Steppe_EMBA only has 10-15% admixture from the post-Mesolithic Near East not including the North Caucasus, and basically all of this comes via female mediated gene flow from farming communities in the Caucasus and perhaps present-day Ukraine.

The relevant blog post from 2016 is here. I totally forgot that I made such a bold prediction. But it actually has a very good chance now of being proven correct, more or less.

This, however, depends on the precise origin of the Yamnaya-like Eneolithic populations of the southernmost parts of the Pontic-Caspian steppe. But, considering the data in Wang et al., I think the possibility that they date back to the Pottery Neolithic period, and are thus indigenous to the region, looks quite high.

About a year later I made a prediction about the genetic structure of the Maykop people, and was basically proven right by Wang et al. (see here). Admittedly, my jaw dropped when I saw how the Steppe Maykop individuals came out in the preprint, with their Botai-like ancestry that is missing in all Yamnaya populations sampled to date. But it was an interesting outcome and nice to be surprised by ancient DNA yet again.

See also...

Genetic borders are usually linguistic borders too

Ahead of the pack

Open thread: What are the linguistic implications of Olalde et al. 2019?

Major horse paper coming soon

Horse domestication is an important and controversial topic, in large part because it's intimately tied to the debate over the location of the Proto-Indo-European (PIE) homeland. Based on the currently available genetic and archaeological data, it seems likely that all modern domesticated horse breeds ultimately derive from the Pontic-Caspian steppe in Eastern Europe (see here and here).

In the interview linked to below (click on the image) horse expert Alan Outram reveals that a new paper will be published within months that will test this theory, and either confirm or debunk it.

Outram also talks about the colonization of Central Asia during the Middle Bronze Age by groups from the west associated with the Sintashta culture. He says that this was probably an aggressive affair, akin to the more recent European colonization of North America, that may have pushed the Botai people, who were the indigenous inhabitants of the Kazakh steppe, and their horses far to the east. This, he suggests, might explain why the Przewalski horse of Mongolia appears to be derived from the Botai horse.

See also...

The mystery of the Sintashta people

Focus on Hittite Anatolia

Friendly Yeniseian steppe pastoralists

Focus on Hittite Anatolia

I computed a series of D-statistics on most of the currently available ancient samples from Central Anatolia - dating from almost the Epipaleolithic (Boncuklu_N) to the Hittite era (Anatolia_MLBA) - to try and get a better idea of who the Indo-European-speaking Hittites may have been. The full output as well as details about the key ancient samples used in this analysis are available here. See anything interesting? The most noteworthy statistics, I suppose, are those listed below, because they're significant (Z≥3) and organized chronologically.

However, the thing to keep in mind in regards to D-statistics, and the very similar f4-statistics, when looking for signals of mixture is that they may or may not produce significant Z scores because of several reasons, such as the choice of the outgroup, the choice of the reference samples and the phylogenetic relationship between them, or even the type, quality and density of the data being used.

Perhaps ironically, the D-statistics above suggest that the Neolithic Central Anatolians (Boncuklu_N and Tepecik_Ciftlik_N) were more European-like than those from the Bronze Age, and I suspect that this is one of the main reasons why the idea of Eastern European admixture (from the Pontic-Caspian steppe and/or Balkans) in Hittites is currently being rejected by the geneticists working on the problem. But this dilemma is easy to explain away by the fact that the Neolithic samples carry much higher ratios of Anatolian Epipaleolithic hunter-gatherer admixture and also other types of ancestry shared with and/or closely related to European hunter-gatherers and early farmers.

In other words, I'd say that most of the statistics are being confounded by deep phylogenetic relationships, and thus aren't very useful for solving the Hittite problem. Interestingly, though, that relationship to Europe is reversed somewhat in the D-statistics involving Anatolia_EBA and Anatolia_MLBA, with the latter showing significantly higher affinity to Eastern European Hunter-Gatherers (EHG) and Minoans.

Thus, in my opinion, to get a more complete picture it's also useful to look for patterns in the statistics, even those that, strictly speaking, don't reach significance. One way to do that is with linear models. So here are a few linear models based on some of my D-statistics. The relevant datasheet is available here.

Arguably, the most striking thing about these models is the position at the top of the graphs of the ancient populations from Central Asia and what is now Iran, and the gradually lower position of populations with progressively less of this type of ancestry. The most plausible explanation for this phenomenon is post-Boncuklu_N gene flow into Central Anatolia from the east, possibly as a continuation of something that was happening already since the Epipaleolithic, but becoming more intense during the Neolithic revolution, probably as a result of rapid population growth in and around the Fertile Crescent.

Indeed, I strongly suspect that one of the main reasons why we've been hearing so much lately about Iran as a likely candidate for the Indo-European homeland is this strong eastern signal in Bronze Age Anatolian DNA. If so, then this is likely to be a misunderstanding, because there are better explanations for it than the Indo-Europeans, such as the Hattians and Hurrians.

Another rather obvious outcome in my graphs is the relatively stronger affinity between the Bronze Age Anatolians and the ancient populations from Eastern Europe, including, and especially, those from the Pontic-Caspian steppe, compared to Tepecik_Ciftlik_N. In fact, looking at the Anatolia_EBA vs Tepecik_Ciftlik_N graph, I'd say that steppe admixture was already seeping into Central Anatolia during the Early Bronze Age.

If so, this is an important point that should be taken into account when modeling the ancestry of the Hittite era Anatolians. That's because if Anatolia_EBA already harbored some steppe ancestry, then we'd be shooting ourselves in the proverbial foot if we were to use it as the supposedly unadmixed reference population to try and determine whether Anatolia_MLBA was partly of steppe origin. Hence, to model the ancestry of Anatolia_MLBA, at least in the context of possible migrations from the steppe to Anatolia during the Bronze Age, it might be more useful to use Tepecik_Ciftlik_N as the likely unadmixed reference population.

Let's try that with qpAdm, first on the whole Anatolia_MLBA set, and then on one individual labeled MA2203, who, as far as I can tell, shows an elevated level of steppe ancestry in several different types of analyses. I chose Yamnaya_Kalmykia as the potential mixture source from the steppe because it's likely to be the closest available population in my dataset to the Eneolithic groups of the southern region of the Pontic-Caspian steppe.

Anatolia_MLBA
Seh_Gabi_ChL 0.200±0.043
Tepecik_Ciftlik_N 0.659±0.033
Yamnaya_Kalmykia 0.141±0.022
chisq: 11.425
tail prob: 0.408405
Full output

MA2203
Seh_Gabi_ChL 0.179±0.065
Tepecik_Ciftlik_N 0.622±0.049
Yamnaya_Kalmykia 0.199±0.036
chisq: 12.914
tail prob: 0.299004
Full output

Please note, however, that these mixture models are based on f4-statisctics. So, obviously, they're going to be affected by the same factors as described above that affect f4-statistics. Hence, despite the seemingly statistically sound output, the steppe admixture that you see there might not actually be admixture from the steppe.

In fact, there's a good reason why I'm not shouting from the rooftops that I've just uncovered the presence of steppe ancestry in Bronze Age Anatolia, and thus confirmed the steppe or kurgan hypothesis positing that the Hittite and indeed Indo-European homeland was located in the Pontic-Caspian steppe. That's because I used a mixed bag of UDG-treated capture data and non-UDG-treated shotgun data. This is known to be a serious problem, which can skew the results of even the most robust analyses, and produce spurious statistics and Z scores.

Nevertheless, I'm reasonably confident that my findings will eventually be confirmed with more and higher quality data from ancient Anatolia. Let's wait and see.

See also...

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

Global25 workshop 3: genes vs geography in Northern Europe

To produce the intra-North European Principal Components Analysis (PCA) plot below, download this datasheet, plug it into the PAST program, which is freely available here, then select all of the columns by clicking on the empty tab above the labels, and choose Multivariate > Ordination > Principal Components or Discriminant Analysis. This is what you should end up with...

I'd say that the result more or less resembles a geographic map of Northern Europe. Of course, if you're in the possession of your own personal Global25 coordinates, you can add yourself to this plot to check whether your position matches your geographic origin.

Please keep in mind, however, that the vast majority (>90%) of your ancestry must be from north of the Alps, Balkans and Pyrenees to obtain a sensible outcome. Also please ensure that all of the columns in the datasheet are filled out correctly, including the group column, otherwise your position on the plot will be skewed.

See also...

Global25 workshop 1: that classic West Eurasian plot

Global25 workshop 2: intra-European variation

Global25 workshop 4: a neighbour joining tree

Getting the most out of the Global25

Genetic ancestry online store (to be updated regularly)

The South Asian cline that no longer exists

Before the Indo-Europeans and Austroasiatics got to South Asia, probably well within the last 4,000 years, it's likely that all of the genetic variation in the region basically sat along a genetic cline devoid of any Bronze Age steppe and Southeast Asian ancestry, like the one in the Principal Component Analysis (PCA) below running from the Paniya to the "Indus Periphery" ancient sample Shahr_I_Sokhta BA2.

Note that almost all of the South Asian populations, including the Iron Age (IA) Swat Valley groups, are clearly peeling away from the said cline towards the Tajiks, in other words towards Central Asia. This is a reflection of the widespread presence of Sintashta-related steppe admixture among South Asians, especially those speaking Indo-European languages. Moreover, the Bangalis and Burushos are being pushed towards the top left of the plot as a result of East Asian-related ancestry. In the case of the former, this is largely due to gene flow from Austroasiatic groups.

It'll be interesting to see how ancient Harappans behave in this analysis. I'm betting that they'll be very similar to the Indus Periphery trio, although judging by the latest press report on the topic (see here), the Harappan samples from Rakhigarhi might be shifted much closer to the Paniya as a result of a higher ratio of indigenous South Asian ancestry.

The PCA is based on my Global25 test. If you're South Asian and in the possession of Global25 coordinates, you can add yourself to this plot using the datasheet available here. Plug the datasheet into the PAST program (freely available here), select all of the columns, and go Multivariate > Ordination > Principal Components (PCA).

Update 10/08/2018: I managed to almost reproduce my PCA with a graph based on D-stats of the form D(Mbuti,X)(Onge,Ganj_Dareh_N)/D(Mbuti,X)(Ganj_Dareh_N,Sintashta_MLBA). Admittedly, Gonur2_BA didn't want to cooperate by pushing slightly up and away from the ghost South Asian cline. But this may have been due to a lack of data or perhaps minor admixture (keep in mind that this sample is actually from Turkmenistan and not South Asia). However, combining all three of the Indus_Periphery individuals worked well enough. The relevant datasheet is available here.

See also...

Global25 workshop 1: that classic West Eurasian plot

Global25 workshop 2: intra-European variation

Global25 workshop 3: genes vs geography in Northern Europe

Global25 workshop 4: a neighbour joining tree

Getting the most out of the Global25

Genetic ancestry online store (to be updated regularly)

A Mycenaean and an Iron Age Iranian walk into a bar...

What do they have in common? The same type of Near Eastern ancestry? From Iran? Nope, that's a joke. Obviously, they share the same type of steppe ancestry. This probably has some very important linguistic implications.

The relevant Principal Component Analysis (PCA) datasheet is available here. Below are two pairs of formal mixture models that support my inferences from the PCA.

Mycenaean
Srubnaya_MLBA 0.266±0.029
Tepecik_Ciftlik_N 0.734±0.029
taildiff: 0.588000631
Full output

Mycenaean
Minoan_Lasithi 0.790±0.023
Srubnaya_MLBA 0.210±0.023
taildiff: 0.187709803
Full output

...

Turkmenistan_IA
Namazga_CA 0.528±0.040
Srubnaya_MLBA 0.472±0.040
taildiff: 0.561330411
Full output

Turkmenistan_IA
Dzharkutan1_BA 0.530±0.037
Srubnaya_MLBA 0.470±0.037
taildiff: 0.485083377
Full output

But seriously, what's the direct link between populations like Tepecik_Ciftlik_N/Minoan_Lasithi and Namazga_CA/Dzharkutan1_BA, except some exceedingly distant farmer ancestry from the Fertile Crescent?

See also...

An early Iranian, obviously

Graeco-Aryan parallels

Yamnaya isn't from Iran just like R1a isn't from India

An early Iranian, obviously

Today, the part of Asia between the Caspian Sea and the Altai Mountains, known as Turan, is largely a Turkic-speaking region. But during the Iron Age it was dominated by Iranian speakers. Throughout this period it was the home of a goodly number of attested and inferred early Iranic peoples, such as the Airya, Dahae, Kangju, Massagetae, Saka and Sogdians.

Indeed, the early Iron Age Yaz II archaeological culture, located in southwestern Turan, is generally classified as an Iranian culture, and even posited to have been the Airyanem Vaejah, aka home of the Iranians, from ancient Avestan literature.

That's not to say that Iranian speakers weren't present in this part of the world much earlier. They probably were, and it's likely that we already have their genomes (see here). But the point I'm making is that Turan can't be reliably claimed to have been an Iranian realm until the Iron Age.

Ergo, any ancient DNA samples from Turan dating to the Iron Age, as opposed to, say, the Bronze Age, are very likely to be those of early Iranian speakers. One such sample is Turkmenistan_IA DA382 from Damgaard et al. 2018.

Below is a screen cap of the "time map" from homeland.ku.dk, with the slider moved to 847 BC, showing the location of the burial site where the remains of DA382 were excavated. The site is marked with the Z93 label because DA382 belongs to the Eastern European-derived Y-chromosome haplogroup R1a-Z93. Interestingly, his burial was located in close proximity to archaeological sites associated with the above mentioned and contemporaneous Yaz II culture.

DA382 didn't get much of a run in the Damgaard et al. paper, and little wonder because the authors also analyzed 73 other ancient samples. So let's take a close look at this individual's genetic structure to see whether there's anything particularly Iranian about it.

Damgaard et al. did mention that DA382 was partly of Middle to Late Bronze Age (MLBA) steppe origin. And indeed, my own mixture models using qpAdm confirm this finding with very consistent results and strong statistical fits. Here are a couple of two-way examples...

Turkmenistan_IA
Namazga_CA 0.528±0.040
Srubnaya_MLBA 0.472±0.040
taildiff: 0.561330411
Full output

Turkmenistan_IA
Dzharkutan1_BA 0.530±0.037
Srubnaya_MLBA 0.470±0.037
taildiff: 0.485083377
Full output

The fact that the MLBA Srubnaya samples from the Pontic-Caspian steppe can be used to model DA382's ancestry (alongside Bronze and Copper Age populations from Turan) with such ease shouldn't be surprising, considering the he belongs to R1a-Z93, which is the dominant Y-haplogroup in the Srubnaya and all other closely related MLBA steppe peoples.

Now, Srubnaya is generally regarded to be the proto-Iranian archaeological culture. How awesome is that considering those qpAdm fits? But, admittedly, this is just an inference, even if a robust one, based on genetic, archaeological and historical linguistics data. So apart from the fact that DA382 comes from Iron Age Turan, an Iranian-speaking realm, is there any other way to link him directly to Iranians?

Well, he's very similar in terms of overall genetic structure to some of the least Turkic-admixed Iranian speakers still living in Turan, and might well be ancestral to them.

For instance, below is a Principal Component Analysis (PCA) featuring a wide range of ancient and present-day West Eurasian samples. Note that, in line with the qpAdm models, DA382 clusters about half-way between the populations of the MLBA steppe and pre-Kurgan expansion Turan, and amongst present-day Yaghnobi and Pamiri Tajiks. In fact, he clusters at the apex of a southeast > northwest cline made up of Tajiks that appears to be pulling towards Europeans.

Needless to say, Tajiks, especially Pamiri Tajiks, also pack a lot of Srubnaya-related ancestry. I've talked about this plenty of times at this blog (for instance, see here). But what happens if I try to model Pamiri and Yaghnobi Tajiks with DA382?

Tajik
Turkmenistan_IA 0.892±0.023
Han 0.108±0.023
taildiff: 0.794566182
Full output

Wow, it's an awesome fit! My mind's made up: DA382 was probably an Iranian speaker and, more specifically, an Eastern Iranian speaker. Who disagrees and why? Feel free to let me know in the comments (unless you're banned, in which case, f*ck off).

See also...

A Mycenaean and an Iron Age Iranian walk into a bar...

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...

"The Homeland: In the footprints of the early Indo-Europeans" time map

Click HERE to view the interactive time map, and give it some time to load if you're on a slow connection. Use the slider tool to explore different time periods from 6385 BC to 1 BC. It's still a work in progress, so feel free to let the author, Mikkel Nørtoft, know if anything should be added, tweaked and/or generally improved.

Below is a screen cap of the map with the slider moved to 3618 BC. Note the sheep in the North Pontic steppe and the wheels just west of it. Wink, wink, nudge, nudge...

See also...

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

Friendly Yeniseian steppe pastoralists

For most people the Proto-Indo-European (PIE) homeland debate isn't just about language, but also, or even more so, about things like ancestry, politics, racism, and ethnic pride.

I don't want to get into all the dirty details in this post, but, for instance, many of those who argue vehemently against a steppe homeland seem to really hate the idea that their ancestors were, at some level, dominated by a bunch of sheep and cow herders from an obscure part of Eastern Europe. Why? I'm pretty sure because they find this humiliating.

Hence, PIE homeland debates are generally very emotional and often degenerate into shouting matches. So what would happen if we assumed that those sheep herders weren't Indo-Europeans? Let's say, for the sake of argument, that they spoke extinct Yeniseian languages.

Well, nothing really...

We still have them expanding in a big way out of the Pontic-Caspian steppe. And the fact that their impact was mostly male mediated, especially at the two ends of its range, in Iberia and India, suggests that they weren't just friendly pastoralists looking for new grazing fields.

In fact, in India, steppe ancestry, including Y-chromosome haplogroup R1a, is much more pronounced in the upper castes than in the rest of society. But who knows what that means, right? Maybe those friendly "Yeniseian" steppe pastoralists just got lucky or something?

But that's OK, perhaps this will always remain a mystery? In any case, does anyone know if there's any sort of Yeniseian substrate in Celtic or Mycenaean? Haha.

See also...

"Heavily sex-biased" population dispersals into the Indian Subcontinent (Silva et al. 2017)

Migration of the Bell Beakers—but not from Iberia (Olalde et al. 2018)

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

Ahead of the pack

Eurogenes Blog January 2018 (see here):

Yamnaya and other similar Eneolithic/Bronze Age herder groups from the Eurasian steppe were mostly a mixture of Eastern European Hunter-Gatherers (EHG) and Caucasus Hunter-Gatherers (CHG). But they also harbored minor ancestry from at least one, significantly more westerly, source that pulled them away from the EHG > CHG north/south genetic cline.

...

It's interesting and, I'd say, important to note that the West Asian reference groups produce amongst the worst statistical fits (in bold text). What this suggests is that Yamnaya did not harbor extra West Asian ancestry on top of its CHG input.

...

Rather, Blatterhole_MN is simply the best proxy in this analysis for the non-CHG/EHG ancestry in Yamnaya, and the important question is why?

Considering also the presence at the top of the list of Koros_HG (which includes Hungary_HG I1507), Germany_MN and Vinca_MN, the likely answer is its high ratio of Western European Hunter-Gatherer (WHG) ancestry.

...

So is the missing piece of the Yamnaya puzzle a population with roughly equal ratios of Early Neolithic (EN) and WHG ancestries from the Carpathian Basin or surrounds? Quite possibly. But let's wait and see what happens when I add the ancient groups from the Balkans and North Pontic steppe from the forthcoming Mathieson et al. 2018 to this analysis.

And now Wang et al. May 2018 (see here).

In principal component space Eneolithic individuals (Samara Eneolithic) form a cline running from EHG to CHG (Fig. 2D), which is continued by the newly reported Eneolithic steppe individuals.

...

However, PCA results also suggest that Yamnaya and later groups of the West Eurasian steppe carry some farmer related ancestry as they are slightly shifted towards ‘European Neolithic groups’ in PC2 (Fig. 2D) compared to Eneolithic steppe.

...

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).

...

We find that Yamnaya individuals from the Volga region (Yamnaya Samara) have 13.2±2.7% and Yamnaya individuals in Hungary 17.1±4.1% Anatolian farmer-related ancestry (Fig.4; Supplementary Table 18)– statistically indistinguishable proportions. Replacing Globular Amphora by Iberia Chalcolithic, for instance, does not alter the results profoundly (Supplementary Table 19). This suggests that the source population was a mixture of Anatolian farmer-related ancestry and a minimum of 20% WHG ancestry, a profile that is shared by many Middle/Late Neolithic and Chalcolithic individuals from Europe of the 3 rd millennium BCE analysed thus far.

Strikingly similar, don't you think? However, I'm not implying that they copied me. The point I'm making is that I predicted this outcome ahead of anyone else, and was able to demonstrate it without some of the key ancient samples that Wang et al. had access to. Indeed, kudos to them for finding and successfully sequencing those all important new Eneolithic steppe samples.

Moreover, these results mean that it's no longer plausible to argue that the Yamnaya population, by and large, formed due to recent gene flow from south of the Caucasus, let alone from what is now Iran, into the Pontic-Caspian steppe. Obviously, this is a major problem for anyone arguing that the Proto-Indo-European (PIE) homeland may have been located somewhere south of the Caucasus, such as Paul Heggarty of the Max Planck Institute for the Science of Human History (for instance, see here). But hey, never mind the facts when you have an awesome theory, right?

See also...

Yamnaya: home-grown

Genetic borders are usually linguistic borders too

Yamnaya isn't from Iran just like R1a isn't from India