The G25 Proto-Indo-European master sheet

I'm putting together a G25 Proto-Indo-European master sheet that I'll be using in a future blog post about the Indo-European, or, if you wish, Indo-Anatolian homeland.

An early version of the master sheet is available HERE. Please note, the first pop label is my own while the second one is from the v66.2M.AADR dataset.

I'm aiming to expand it significantly and update it regularly. Below is a Vahaduo G25 West Eurasia PCA with all the samples. What am I missing? Feel free to let me know in the comments.

Spoiler alert! Here are a few of the revelations that you can expect in the aforementioned blog post about the Indo-European homeland:

- Yamnaya is almost certainly derived from Serednii Stih (aka Sredny Stog). I've been talking about this for years and you can probably pick it up without too much trouble in the PCA above. Finally, even Iosif Lazaridis, David Reich, Nick Patterson and friends are now on board with this idea as per their latest paper on the topic (see Lazaridis et al. 2025).

- However, I'm not convinced by the Lazaridis et al. hypothesis that the Caucasus–lower Volga (CLV) cline is intimately linked to the Indo-Anatolian and proto-Anatolian expansions. That's because the CLV cline is an artifact of isolation-by-distance working for thousands of years across a vast and highly diverse landscape, and it includes a wide range of populations that usually have nothing to do with each other.

- The question of who actually spoke Indo-Anatolian first will, in all likelihood, never be solved to everyone's satisfaction. But the number of true candidate groups is actually quite small, and I reckon they're almost certainly all highlighted in my PCA above. Wink, wink, nudge, nudge.

See also...

The Caucasus is a semipermeable barrier to gene flow

The Nalchik surprise

If, like Iosif Lazaridis, you subscribe to the idea that the Yamnaya people carry early Anatolian farmer-related admixture that spread into Eastern Europe via the Caucasus, then I've got great news for you.

We now have a human sample from the Eneolithic site of Nalchik in the North Caucasus, labeled NL122, that packs well over a quarter of this type of ancestry (see here). Below is a quick G25/Vahaduo model to illustrate the point (please note that Turkey_N = early Anatolian farmers).

Target: Nalchik_Eneolithic:NL122
Distance: 2.1934% / 0.02193447
60.8 Russia_Steppe_Eneolithic
26.2 Turkey_N
13.0 Georgia_Kotias

On the other hand, if, again like Iosif Lazaridis, you subscribe to the idea that the Indo-European language spread into Eastern Europe via the Caucasus in association with this early Anatolian farmer-related admixture, then I've got terrible news for you.

That's because NL122 is apparently dated to a whopping 5197-4850 BCE (see here). This dating might be somewhat bloated, possibly due to what's known as the reservoir effect, because the Nalchik archeological site is generally carbon dated to 4840–4820 BCE.

However, even with the younger dating, this would still mean that early Anatolian farmer-related ancestry arrived in the North Caucasus, and thus in Eastern Europe, around 4,800 BCE at the latest. That's surprisingly early, and just too early to be relevant to any sort of Indo-European expansion from a necessarily even earlier Proto-Indo-Anatolian homeland somewhere south of the Caucasus.

This means that NL122 effectively debunks Iosif Lazaridis' Indo-Anatolian hypothesis. Unless, that is, Iosif can provide evidence for a more convoluted scenario, in which there are at least two early Anatolian farmer-related expansions into Eastern Europe via the Caucasus, and the expansion relevant to the arrival of Indo-European speech came well after 5,000 BCE.

I haven't done any detailed analyses of NL122 with formal stats and qpAdm. But my G25/Vahaduo runs suggest that it might be possible to model the ancestry of the Yamnaya people with around 10% admixture from a population similar to NL122.

Target: Russia_Samara_EBA_Yamnaya
Distance: 3.4123% / 0.03412328
72.6 Russia_Progress_Eneolithic
18.2 Ukraine_N
9.2 Nalchik_Eneolithic

However, I don't subscribe to the idea that the Yamnaya people carry early Anatolian farmer-related admixture that spread into Eastern Europe via the Caucasus (on top of what is already found in Progress Eneolithic). Based on basic logic and a wide range of my own analyses, I believe that they acquired this type of ancestry from early European farmers, probably associated with the Trypillia culture. For instance...

Target: Russia_Samara_EBA_Yamnaya
Distance: 3.2481% / 0.03248061
80.2 Russia_Progress_Eneolithic
13.6 Ukraine_Neolithic
6.2 Ukraine_VertebaCave_MLTrypillia
0.0 Nalchik_Eneolithic

Another way to show this is with a Principal Component Analysis (PCA) that highlights a Yamnaya cline made up of the Yamnaya, Steppe Eneolithic and Ukraine Neolithic samples. As you can see, dear reader, there's no special relationship between the Yamnaya cline and Nalchik_Eneolithic. The Yamnaya samples, which are sitting near the eastern end of the Yamnaya cline, instead seem to show a subtle shift towards the Trypillian farmers.

Indeed, I also don't exactly understand the recent infatuation among many academics, especially Iosif Lazaridis and his colleagues, with trying to put the Proto-Indo-Anatolian homeland somewhere south of the Caucasus. Considering all of the available multidisciplinary data, I'd say it still makes perfect sense to put it in the Sredny Stog culture of the North Pontic steppe, in what is now Ukraine.

Please note that all of the G25 coordinates used in my models and the PCA are available HERE.

See also...

The Caucasus is a semipermeable barrier to gene flow

The Caucasus is a semipermeable barrier to gene flow

The scientists at the David Reich Lab are a clever bunch. But they're not always on top of things, and this can be a problem.

For instance, they fail to understand that the Caucasus has effectively stymied human gene flow between Eastern Europe and West Asia through the ages. That is, the Caucasus is a semipermeable barrier to human gene flow.

Until they accept and understand this fact, they won't be able to accurately characterize the ancestry of the ancient human populations of the Pontic-Caspian (PC) steppe, including the Yamnaya people.

In turn, they also won't be able to locate the Indo-Anatolian homeland.

Now, the Caucasus isn't a barrier to gene flow because it's difficult to cross, and, indeed, many human populations have managed to cross it since the Upper Palaeolithic. As a result, the peoples of the North Caucasus are today genetically more similar to the populations of the Near East than Europe.

In fact, the clear genetic gap between most West Asian and Eastern European populations through the ages is actually caused by the extreme differentiation between the mountain ecology of the Caucasus and the steppe ecology of the PC steppe.

That is, the Caucasus is ecologically so different from the PC steppe that it has been practically impossible for human populations to make the transition from one to the other.

Indeed, it's important to understand that there's no reliable record of any prehistoric human population successfully making the transition from the mountain ecology to the steppe ecology in this part of the world.

In other words, contrary to claims by people like David Reich and David Anthony, there's no solid evidence of any significant prehistoric human migration from the Caucasus, or from south of the Caucasus, to Eastern Europe by hunter-gatherers, farmers or pastoralists.

But, you might ask, how on earth did the Yamnaya people get their significant Caucasus/Iranian-related admixture if not via a mass migration from the Caucasus and/or the Iranian Plateau, as is often argued by the above mentioned scholars and their many colleagues?

Well, obviously, the diffusion of alleles from one population to another can happen without migration. All that is needed is a contact zone between them.

The ancient DNA and archeological data currently available from the Caucasus and the PC steppe suggest to me that there was at least one such contact zone in this area bringing together the peoples of the mountain and steppe ecoregions. This allowed them to mix, probably gradually and over a long period of time, by and large without leaving their ecoregions.

Once the Caucasus alleles entered the steppe, they were spread around by local hunter-gatherers and pastoralists who were highly mobile and well adapted to the steppe ecology.

Someone should write a paper about this.

See also...

The Nalchik surprise

Understanding the Eneolithic steppe

Matters of geography

The story of the Khvalynsk people

I'm totally serious when I say that this video is more objective, informative and accurate than any peer-reviewed paper published to date when it comes to the genetic origins of the Khvalynsk people.

However, that's not to say it's perfect. I think it misses some important details. See here...

The Caucasus is a semipermeable barrier to gene flow

Dear David, Nick, Iosif...let's set the record straight

Understanding the Eneolithic steppe

Dear Sandra, Wolfgang...a problem

In their recent paper, titled Early contact between late farming and pastoralist societies in southeastern Europe, Penske et al. make the following claim:

By contrast, Yamnaya Caucasus individuals from the southern steppe can be modelled as a two-way model of around 76% Steppe Eneolithic and 26% Caucasus Eneolithic/Maykop, confirming the findings of Lazaridis and colleagues 47. This two-way mix (40% + 60%, respectively) also provides a well-fit model (P = 0.09) for the Ozera outlier individual, consistent with the position in PCA and corroborating an influence from the Caucasus.

Err, nope.

The Ozera Yamnaya outlier, a female dated to 3096-2913 calBCE, is, in fact, a ~50/50 mix between standard Yamnaya and Late Maykop. It's a result that is totally unambiguous.

There are a number of ways to demonstrate this fact. For example, with the qpAdm software that was also used by Penske et al., except with different outgroups or right pops. Please note that in my dataset the Ozera outlier is labeled Ukraine_Ozera_EBA_Yamnaya_o.

right pops:
Cameroon_SMA
Levant_N
Iran_GanjDareh_N
Iran_C_SehGabi
Georgia_HG
Turkey_N
Serbia_IronGates_Mesolithic
Russia_WestSiberia_HG
Russia_Karelia_HG
Latvia_HG
Russia_Boisman_MN
Brazil_LapaDoSanto_9600BP

Ukraine_Ozera_EBA_Yamnaya_o
Russia_Caucasus_EneolithicMaykop 0.554±0.031
Russia_Steppe_Eneolithic 0.446±0.031
P-value 0.00109868 (FAIL)

Ukraine_Ozera_EBA_Yamnaya_o
Russia_LateMaykop 0.512±0.035
Russia_Samara_EBA_Yamnaya 0.488±0.035
P-value 0.462447 (PASS)

I can also do it with the Global25/Vahaduo method. And you, dear reader, can too, by putting the Target and Source Global25 coords from the text file here into the relevant fields here.

Target: Ukraine_Ozera_EBA_Yamnaya_o
Distance: 2.9292% / 0.02929202
50.6 Russia_Samara_EBA_Yamnaya
49.4 Russia_Caucasus_LateMaykop
0.0 Russia_Caucasus_EneolithicMaykop
0.0 Russia_Steppe_Eneolithic

Moreover, here's a self-explanatory Principal Component Analysis (PCA) plot that illustrates why my Late Maykop/Samara Yamnaya combo is much better than the reference populations used by Penske and colleagues. It was done with the PCA tools here.

I'm pointing this out for two main reasons. First of all, this is a fairly obvious mistake that should've been avoided, especially considering the level of expertise and experience among the authors (such as Wolfgang Haak and Johannes Krause).

Secondly, it's important to understand that the Ozera outlier comes out almost exactly 50% Samara Yamnaya because the standard Yamnaya genotype already existed well before she was alive, and thus she cannot be used to corroborate any sort of influence from the Caucasus in the formation of the mainstream Yamnaya population.

As for the Yamnaya Caucasus individuals, I don't know why Penske et al. attempted to model their ancestry as a group, because they don't form a coherent genetic cluster. RK1001 and ZO2002 are fairly similar to standard Yamnaya samples, while RK1007 and SA6010 resemble Eneolithic steppe samples from the Progress burial site. This is what happens when I try to reproduce the Penske et al. model with my outgroups.

Russia_Caucasus_EBA_Yamnaya
Russia_Caucasus_EneolithicMaykop 0.187±0.019
Russia_Steppe_Eneolithic 0.813±0.019
P-value 4.15842e-06 (HARD FAIL)

Oh, and Penske et al. modeled the ancestry of mainstream Yamnaya as a three-way mixture with Steppe Eneolithic, Caucasus Eneolithic/Maykop and Ukraine Neolithic (or Ukraine N). They succeeded, but with my outgroups it's another hard fail.

Russia_Samara_EBA_Yamnaya
Russia_Caucasus_EneolithicMaykop 0.177±0.017
Russia_Steppe_Eneolithic 0.706±0.026
Ukraine_N 0.116±0.014
P-value 4.73919e-07 (HARD FAIL)

Admittedly, proximal models aren't easy to get right. And if you throw enough outgroups into a model, a large proportion of plausible models will fail. But I'm somewhat taken aback by these poor statistical fits.

In my opinion, mainstream Yamnaya doesn't harbor any Caucasus ancestry that wasn't already present on the Pontic-Caspian steppe during the Eneolithic or even much earlier (see here). But ultimately this problem can only be solved with direct evidence from ancient DNA, so let's now wait patiently for the right samples.

Citation...

Penske et al., Early contact between late farming and pastoralist societies in southeastern Europe, Nature, https://doi.org/10.1038/s41586-023-06334-8

See also...

Understanding the Eneolithic steppe

Dear David, Nick, Iosif...let me tell you about Yamnaya

Lazaridis, Alpaslan-Roodenberg et al. recently claimed that the Yamnaya people of the Pontic-Caspian (PC) steppe carried "substantial" ancestry from what is now Armenia or surrounds.

However, this claim is essentially false.

Only one individual associated with the Yamnaya culture shows an unambiguous signal of such ancestry. This is a female usually labeled Ukraine_Yamnaya_Ozera_o:I1917. The "o" suffix indicates that she is an outlier from the main Yamnaya genetic cluster.

Unlike I1917, typical Yamnaya individuals carry a few per cent of ancient European farmer admixture. This ancestry is only very distantly Armenian-related via Neolithic Anatolia (see here).

It's difficult for me to understand how Lazaridis, Alpaslan-Roodenberg et al. missed this. I suspect that they relied too heavily on formal statistics and overinterpreted their results.

Formal statistics are a very useful tool in ancient DNA work. Unfortunately, they're also a relatively blunt tool that often has problems distinguishing between similar sources of gene flow.

There are arguably better methods for studying fine scale ancestry, such as Principal Component Analysis (PCA).

Below is a somewhat special PCA featuring a wide range of ancient populations that plausibly might be relevant to the genetic origins of the Yamnaya people. Unlike most PCA with ancient samples, this PCA doesn't rely on any sort of projection, so that all of the actors are interacting with each other and directly affecting the outcome.

Here's another version of the same plot with a less complicated labeling system. Note that I designed this PCA specifically to differentiate between European populations and those from the Armenian highlands, the Iranian plateau and surrounds.

And here's a close up of the part of the plot that shows the Yamnaya cluster. This cluster is made up of samples associated with the Afanasievo, Catacomb, Poltavka and Yamnaya cultures. All of the individuals in this part of the plot are closely related, which is why they're so tightly packed together. The differentiation between them is caused by admixture from different groups mostly from outside of the PC steppe.

The Yamnaya cluster can be broadly characterized as a population that formed along the genetic continuum between the Eneolithic groups of the Progress region and Neolithic foragers from the Dnieper River valley (Progress_Eneolithic and Ukraine_N, respectively). However, this cluster also shows a slight western shift that is increasingly more pronounced in the Corded Ware samples. This shift is due to the aforementioned admixture from early European farmers.

Indeed, the plot reveals two parallel clines extending west from the Progress samples. One of the clines is made up of the Yamnaya cluster and the Corded Ware samples, and pulls towards the ancient European farmers. The other cline includes Ukraine_Yamnaya_Ozera_o:I1917 and pulls towards samples from the Armenian highlands and surrounds.

Being aware of these two clines and knowing how they came about is important to understanding the genetic prehistory of the PC steppe and indeed of much of Eurasia.

At some point, probably during the late Eneolithic, a Progress-related group experienced gene flow from the west and became the Yamnaya and Corded Ware populations. Sporadically, admixture from the Armenian highlands and the Iranian plateau also entered the PC steppe, giving rise to people like the Steppe Maykop outliers and Ukraine_Yamnaya_Ozera_o:I1917.

Unfortunately, this sort of PCA doesn't offer output suitable for mixture modeling, basically because the recent genetic drift shared by many of the samples creates significant noise.

However, to check that my inferences based on the plot are correct I can create composites with specific ancestry proportions to see how they behave. In the plot below Mix1 is 80% Progress_Eneolithic and 20% Iran_Hajji_Firuz_N, Mix2 is 80% Progress_Eneolithic and 20% Armenia_EBA_Kura_Araxes, while Mix3 is 80% Progress_Eneolithic, 15% Ukraine_N and 5% Hungary_MN_Vinca (Middle Neolithic farmers from the Carpathian Basin).

Obviously, we can't get Yamnaya by mixing Progress_Eneolithic with any ancients from the Armenian highlands or the Iranian plateau. On the other hand, Mix3 works quite well, at least in the first two dimensions. In some of the other dimensions genetic drift specific to Ukraine_N pulls it away from the Yamnaya cluster, but this is to be expected.

By the way, the plots were created with the excellent Vahaduo Custom PCA tool freely available here. It's well worth trying the interactive 3D option using my PCA data. The relevant datasheet is available here.

See also...

Dear David, Nick, Iosif...let's set the record straight

The Caucasus is a semipermeable barrier to gene flow

The story of R-V1636

Who wants to bet against this map? Keep in mind that ART038 (~3000 calBCE) remains the oldest sample with the V1636 and R1b Y-chromosome mutations in the West Asian ancient DNA record. Ergo, there's nothing to suggest that V1636 or R1b entered Eastern Europe from West Asia.

See also...

A tantalizing link

How relevant is Arslantepe to the PIE homeland debate?

The Kura-Araxes people deserve better

When discussing the Kura-Araxes culture and its people it's important to understand these key points:

- there is Eastern European steppe ancestry in Kura-Araxes samples, and if you're not seeing it then you're not looking hard enough

- Armenian Kura-Araxes samples are mainly a mixture between three different groups currently best represented in the ancient DNA record by ARM_Areni_C, IRN_Hajji_Firuz_C and RUS_Darkveti-Meshoko_En

- ergo, most of the steppe ancestry in the Kura-Araxes population of what is now Armenia must have been mediated via local Chalcolithic groups like ARM_Areni_C

- Kura-Araxes samples show Mesopotamian-related ancestry, and this mustn't be ignored.

Oh, you don't believe it because you just read a big paper in Science claiming otherwise?

Well, the authors of that paper, Lazaridis, Alpaslan-Roodenberg et al., used distal mixture models to study the ancestry of their Kura-Araxes samples, and such models can miss important details.

Consider these three proximate mixture models for a relatively high quality and very homogenous Kura-Araxes sample set from the aforementioned paper. They were done with the qpAdm software

ARM_Kura-Araxes_Berkaber
ARM_Areni_C 0.239±0.068
IRN_Hajji_Firuz_C 0.379±0.068
RUS_Darkveti-Meshoko_En 0.382±0.054
P-value 0.285122 (Pass)
Full output

ARM_Kura-Araxes_Berkaber
IRN_Hajji_Firuz_C 0.569±0.051
RUS_Darkveti-Meshoko_En 0.363±0.058
RUS_Progress_En 0.068±0.020
P-value 0.20306 (Pass)
Full output

ARM_Kura-Araxes_Berkaber
IRN_Hajji_Firuz_C 0.531±0.060
RUS_Darkveti-Meshoko_En 0.469±0.060
P-value 0.0132579 (Fail)
Full output

Some caveats apply. For instance, the pass threshold (P-value ≥0.05) is arbitrary. But the point is that the models look much better with steppe-related and steppe reference populations (ARM_Areni_C and RUS_Progress_En, respectively).

Moreover, the unique and vital Darkveti-Meshoko population is represented by just one individual. I also have the genotypes of his brother and sister, but relatives aren't allowed in these sorts of tests.

Including a singleton in the analysis means that I can't use the inbreed: YES option, which apparently can be a bad thing. Nevertheless, these models do look very solid.

Indeed, I can also model ARM_Kura-Araxes_Berkaber as practically 100% RUS_Maykop_Novosvobodnaya, perhaps with some excess ARM_Areni_C-related input.

ARM_Kura-Araxes_Berkaber
ARM_Areni_C 0.094±0.087
RUS_Maykop_Novosvobodnaya 0.906±0.087
P-value 0.284259 (Pass)
Full ouput

This makes good sense, because RUS_Maykop_Novosvobodnaya can also be modeled solidly as a mixture between IRN_Hajji_Firuz_C, RUS_Darkveti-Meshoko_En and RUS_Progress_En.

RUS_Maykop_Novosvobodnaya
IRN_Hajji_Firuz_C 0.614±0.056
RUS_Darkveti-Meshoko_En 0.307±0.064
RUS_Progress_En 0.080±0.022
P-value 0.141468 (Pass)
Full output

I don't know whether the genetic relationship between ARM_Kura-Araxes_Berkaber and RUS_Maykop_Novosvobodnaya shown in my model is due to Maykop ancestry in the former. It might just be a coincidence in the sense that the same or similar processes led to the formation of both groups. Feel free to let me know your thoughts about that in the comments.

The fact that the Kura-Araxes people harbored steppe ancestry might be very important in the debate over the location of the so called Indo-Anatolian homeland. For instance, it's possible that the proto-Anatolian language spread from the North Caucasus into Anatolia via the Kura-Araxes culture.

But, admittedly, such a solution doesn't have strong support from historical linguistics data, which suggest that the Indo-Anatolian homeland was located in what is now Ukraine and that Anatolian speakers entered West Asia via the Balkans:

Indo-European cereal terminology suggests a Northwest Pontic homeland for the core Indo-European languages

See also...

R-V1636: Eneolithic steppe > Kura-Araxes?

Dear Iosif...Yamnaya

But Iosif, what about the Phrygians?

Dear Iosif #3

Back in 2016 I made this prediction about the origins of the Yamnaya people (Steppe_EMBA):

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 is still here. Looking back, my analysis is a bit sloppy and I didn't articulate my ideas too well. But that was a pretty good prediction for its time, and I believe it still has a chance of being confirmed, more or less.

On the other hand, the widely publicized hypothesis that the Yamnaya population is a ~50/50 mixture between indigenous Eastern European hunter-gatherers and Near Eastern or West Asian migrants never looked right to me. So I'm glad that it's now dead and buried.

Those of you not up to date with this topic, all you need to know is that the Yamnaya genotype existed in Eastern Europe at least a thousand years before Yamnaya, and, moreover, the Yamnaya people are largely derived from Eastern European foragers already rich in Near Eastern-related ancestry. The relevant ancient genomes are on the way (for instance, see here).

Nevertheless, the narrative that waves of Near Eastern migrants moved into prehistoric Eastern Europe, leading to the emergence of the Yamnaya culture and even the Proto-Indo-European language, is still being pushed by some notable scientists working with ancient DNA.

My hope is that, considering the latest revelations about the genetic origins of the Yamnaya people, these scientists can embrace a more nuanced view. How about something like this?

- people moved around, and they were especially mobile on the Eastern European steppe from the Eneolithic onwards

- when they made contact they sometimes mixed, so there was admixture between far flung steppe groups

- since population densities on the steppe were low until the Yamnaya period, minor admixture that entered the steppe during the Neolithic and Eneolithic wasn't dilluted easily.

See also...

Dear Iosif #2

But Iosif, what about the Phrygians?

Dear Iosif, about that ~2%

Dear Iosif...Yamnaya

Dear Iosif #2

In my last blog post I made a mistake in my interpretation of this quote from Lazaridis, Alpaslan-Roodenberg et al., because it confused the crap out of me:

However, the complete lack of association of R-haplogroup descendants and EHG ancestry in either Armenia or Iran is consistent with either a massive dilution of EHG ancestry in these populations resulting in the dissociation of Y-chromosome lineages from autosomal ancestry over time, or with a scenario in which R-M269 was not associated with substantial EHG ancestry to begin with.

I thought they meant that they couldn't find any Eastern European hunter-gatherer (EHG) ancestry in samples from Armenia or Iran bearing Y-chromosome R1b-M269.

Of course, they did find EHG ancestry in these individuals, it's just that they couldn't establish an association specifically between this type of ancestry and Y-haplogroup R1b.

That is, males with Y-haplogroup R1b in Armenia, Iran and everywhere else generally show about the same level of EHG ancestry as their ethnic kin with other Y-haplogroups.

But so what? Why mention this when discussing the origins of R1b-M269, when it has absolutely no value in this context?

Y-haplogroups aren't linked directly to autosomal DNA, and Lazaridis, Alpaslan-Roodenberg et al. are obviously aware of this (hence their point about the potential massive dilution of EHG ancestry).

In regards to the origins of R1b-M269, and the provenance of West Asian R1b-M269, the really powerful observation is that R1b-M269 shows up rather late and suddenly in the West Asian ancient DNA record along with EHG and steppe ancestry.

That, and the fact that Eastern Europe is an ancient R1b hotbed (while West Asia a desert), means there's virtually no chance that R1b-M269 is native to West Asia. In other words, there was no R1b-M269 in West Asia until the steppe people brought it there from north of the Caucasus.

See also...

Dear Iosif...

Dear Iosif #3

But Iosif, what about the Phrygians?

Dear Iosif, about that ~2%

Dear Iosif...Yamnaya

Dear Iosif...

Update 29/08/22: Dear Iosif #2

...


I'm skimming through the Lazaridis, Alpaslan-Roodenberg et al. paper that just came out at Science. And I feel like someone punched me in the face.

Nevertheless, I'll try to be diplomatic. Suffice to say, for now, that there's some rather strange stuff in this paper.

The main problem is that the authors are attempting to study fine scale ancestry with a somewhat rough distal model. As a result, they miss important details.

For instance, this quote is from the paper's supplementary PDF file, freely available here.

However, the complete lack of association of R-haplogroup descendants and EHG ancestry in either Armenia or Iran is consistent with either a massive dilution of EHG ancestry in these populations resulting in the dissociation of Y-chromosome lineages from autosomal ancestry over time, or with a scenario in which R-M269 was not associated with substantial EHG ancestry to begin with.

Obviously, EHG means Eastern European Hunter-Gatherer. But why focus on EHG? Surely, this makes little sense when looking at the genetic prehistory of West Asia, because no one ever argued that this region was settled by EHG populations. It was widely settled by Yamnaya-related groups, with already heavily diluted EHG ancestry, during the metal ages.

OK, so the authors are actually aware about the potential dilution of EHG ancestry, but they don't really do anything about it.

If we're looking at the origins of West Asian R1b-M269, and using its association with autosomal DNA components as a guide, then we should be focusing on Yamnaya-related ancestry.

For instance, here's a fine scale ancient ancestry model based on Principal Component Analysis (PCA) data. It shows the ancestry proportions of two relatively high coverage Iron Age males from two different sites in Iran from the Lazaridis, Alpaslan-Roodenberg et al. dataset. Both belong to R1b-M269 and both show significant Yamnaya-related ancestry.

Target: IRN_HajjiFiruz_IA:I2327_all
Distance: 2.2930% / 0.02292994
39.6 Kura-Araxes_ARM_Kaps
24.2 IRN_Ganj_Dareh_N
18.2 Levant_PPNB
12.4 Yamnaya_RUS_Samara
4.4 Anatolia_Tepecik_Ciftlik_N
1.2 Han

Target: IRN_Hasanlu_IA:I4232_all
Distance: 2.5179% / 0.02517895
26.0 IRN_Ganj_Dareh_N
25.6 Kura-Araxes_ARM_Kaps
24.4 Anatolia_Tepecik_Ciftlik_N
15.8 Yamnaya_RUS_Samara
7.6 Levant_PPNB
0.6 IRN_Shahr_I_Sokhta_BA2

As a control, here's an earlier, Chalcolithic sample bearing Y-haplogroup J2b from the same region. Not surprisingly, this individual totally lacks the Yamnaya-related signal.

Target: IRN_HajjiFiruz_ChL:I4241_all
Distance: 2.7938% / 0.02793782
32.6 Kura-Araxes_ARM_Kaps
25.6 IRN_Ganj_Dareh_N
23.6 Anatolia_Tepecik_Ciftlik_N
18.2 Levant_PPNB

Overall, these results make perfect sense. I could probably locate very minor signals of EHG ancestry in the Iron Age samples, but that would be more difficult and much less certain, so I won't bother.

Soon I'll be able to rerun these analyses with Bronze Age samples from Dagestan and surrounds. That should bump up the levels of Yamnaya-related ancestry and improve the statistical fits (wink, wink, nudge, nudge).

Disappointingly, Lazaridis, Alpaslan-Roodenberg et al. go so far as to suggest that R1b-M269 may have originated in West Asia.

However, considering the scores of ancient Eastern European populations rich in R1b-M269 and many near and far related subclades of R1b, this makes no sense whatsoever.

Indeed, contemplating nowadays that R1b-M269 might be native to West Asia, where R1b only starts showing up in the ancient DNA record during the Copper Age, is about as stupid as claiming that gravity doesn't exist.

Largely due to their distal model approach, Lazaridis, Alpaslan-Roodenberg et al. also argue that the Indo-Anatolian homeland was located in what is now Armenia and surrounds. I'm far from convinced that this solution will stand the test of time.

In terms of the more widely accepted theory that the Indo-Anatolian homeland was located on the Pontic-Caspian steppe in Eastern Europe, the most important samples in the paper are the three Bronze Age individuals from Yassitepe in western Anatolia. That's because they're from a region that is traditionally seen as the entry point of Indo-Anatolian speakers into Anatolia from the European steppe via the Balkans.

Interestingly, individual I5737, dated to 2035-1900 calBCE or the Middle Bronze Age, belongs to Y-chromosome haplogroup I2a-P78, which surely must be a signal of European ancestry. I see this as a significant result.

Here's how the trio from Yassitepe look in my fine scale ancient ancestry model. Minor Yamnaya-related ancestry does show up, although, admittedly, it might just be noise in individual I5735.

Target: TUR_Aegean_Izmir_Yassitepe_MBA:I5737
Distance: 2.7507% / 0.02750748
58.4 Anatolia_Barcin_N
20.4 Kura-Araxes_ARM_Kaps
9.2 Anatolia_Tepecik_Ciftlik_N
5.6 IRN_Ganj_Dareh_N
3.8 Yamnaya_RUS_Samara
2.6 Levant_PPNB

Target: TUR_Aegean_Izmir_Yassıtepe_EBA:I5733
Distance: 2.7969% / 0.02796887
52.0 Anatolia_Barcin_N
27.2 Kura-Araxes_ARM_Kaps
8.6 Levant_PPNB
6.2 Yamnaya_RUS_Samara
6.0 IRN_Ganj_Dareh_N

Target: TUR_Aegean_Izmir_Yassıtepe_EBA:I5735
Distance: 3.1270% / 0.03127009
36.0 Kura-Araxes_ARM_Kaps
32.4 Anatolia_Tepecik_Ciftlik_N
26.0 Anatolia_Barcin_N
2.8 IRN_Shahr_I_Sokhta_BA2
1.2 Yamnaya_RUS_Samara
1.0 Levant_PPNB
0.6 MAR_Taforalt

This isn't much, especially considering it's already late 2022, but it's better than nothing. Fortunately, more samples from Bronze Age western Anatolia are on the way (wink, wink, nudge, nudge).

However, I'm not done with the Lazaridis, Alpaslan-Roodenberg et al. dataset yet. I'm planning to spend much more time on this blog in the coming weeks and months and will be using their samples in a wide range of analyses.

Citation...

Iosif Lazaridis, Songül Alpaslan-Roodenberg et al., The genetic history of the Southern Arc:A bridge between West Asia and Europe, Science 377, eabm4247 (2022)

See also...

Dear Iosif #3

But Iosif, what about the Phrygians?

Dear Iosif, about that ~2%

Dear Iosif...Yamnaya

The PIE homeland controversy: February 2022 status report

I think we'll see the emergence of two main competing proto-Indo-European (PIE) homeland theories over the next few years:

- a homeland in the Eneolithic North Caucasus, and the spread of Anatolian languages into West Asia with Maykop-related ancestry

- a homeland in the North Pontic region, possibly within the Eneolithic Sredny Stog archeological culture, and the spread of Anatolian languages into West Asia via the Balkans.

Both theories have support from ancient DNA. Some of it has already been published (for instance, see here).

At this point, I can see myself firmly in the North Pontic camp, even if it turns out that North Pontic-related ancestry only made a fleeting impact on Bronze Age Anatolia.

After all, there's no direct relationship between genes and languages, so to prove that Anatolian languages came from the North Pontic, there's no need for North Pontic-related ancestry to persist in Anatolia, as long as we have solid evidence that people with this type of ancestry moved there at the right time.

In my mind, for now, the Maykop culture provides an excellent explanation for non-Indo-European influences in PIE, and there's no need to make it Indo-European speaking, let alone PIE speaking.

See also...

The PIE homeland controversy: June 2021 status report

Domestic horses were introduced into Anatolia and Transcaucasia during the Bronze Age (Guimaraes et al. 2020)

Over at Science Advances at this LINK. This is a very important paper because it basically eliminates West Asia as the source of the modern domestic horse lineage, which leaves the Pontic-Caspian steppe in Eastern Europe as the only viable option.

It also corroborates the linguistic theory that the Proto-Indo-European homeland was located on the Pontic-Caspian steppe. That's because the horse is a key animal in the Proto-Indo-European pantheon, and it appears in Indo-European mythology in intricate roles. This suggests that the speakers of Proto-Indo-European weren't just familiar with the horse but also managed to domesticate it. From the paper:

Abstract: Despite the important roles that horses have played in human history, particularly in the spread of languages and cultures, and correspondingly intensive research on this topic, the origin of domestic horses remains elusive. Several domestication centers have been hypothesized, but most of these have been invalidated through recent paleogenetic studies. Anatolia is a region with an extended history of horse exploitation that has been considered a candidate for the origins of domestic horses but has never been subject to detailed investigation. Our paleogenetic study of pre- and protohistoric horses in Anatolia and the Caucasus, based on a diachronic sample from the early Neolithic to the Iron Age (~8000 to ~1000 BCE) that encompasses the presumed transition from wild to domestic horses (4000 to 3000 BCE), shows the rapid and large-scale introduction of domestic horses at the end of the third millennium BCE. Thus, our results argue strongly against autochthonous independent domestication of horses in Anatolia.

Guimaraes et al., Ancient DNA shows domestic horses were introduced in the southern Caucasus and Anatolia during the Bronze Age, Science Advances 16 Sep 2020: Vol. 6, no. 38, eabb0030, DOI: 10.1126/sciadv.abb0030

See also...

Armenian Highland population prehistory

A new preprint at bioRxiv claims that some sort of large-scale population movement resulted in the spread of Sardinian-like ancestry into both the Armenian Highland and East Africa during or just after the Middle-Late Bronze Age. See Hovhannisyan et al. here.

In all seriousness, my suggestion is that the authors should familiarize themselves with the scientific concept of the sanity check and then try again.

For what it's worth, here's a brief outline of the population history of the Armenian Highland based on what I've learned about the topic from ancient DNA in recent years:

- overall, the Neolithic populations of the Armenian Highland were surely very similar to the Caucasus_lowlands_LN samples from what is now Azerbaijan from the recent Skourtanioti et al. paper (see here)

- Chalcolithic era migrations from the Pontic-Caspian steppe and/or the North Caucasus introduced steppe ancestry to the Armenian Highland, bringing at least some of its populations closer genetically to those of Eastern Europe (a somewhat outdated but still useful blog post about this subject is found here)

- population expansions during the Early Bronze Age associated with the Kura-Araxes cultural phenomenon, which may have originated in what is now Armenia, resulted in a resurgence of indigenous Caucasus hunter-gatherer (CHG) ancestry across the Caucasus, as well as its spread to many other parts of West Asia (see here)

- another significant pulse of Eastern European admixture affected the Armenian Highland during the Middle-Late Bronze Age and Early Iron Age (see here)

- it's not yet completely clear what happened in the Armenian Highland during the Iron Age in terms of significant genetic shifts, due to the lack of ancient human samples from the region dating to this period, but it's still possible that the speakers of proto-Armenian arrived there from the Balkans at this time

- the present-day Armenian gene pool is the result of the processes described above, as well as later events, such as those associated with the Urartian and Ottoman Empires.

Indeed, it's probably not a coincidence that present-day Armenians cluster more or less between the prehistoric populations from the Armenian Highland and surrounds in the Principal Component Analysis (PCA) below.

To see a more detailed and interactive version of the plot, copy paste the data from the text file here into the relevant field at the Vahaduo Globabl25 PCA Views here.

Citation...

Hovhannisyan et al., AN ADMIXTURE SIGNAL IN ARMENIANS AROUND THE END OF THE BRONZE AGE REVEALS WIDESPREAD POPULATION MOVEMENT ACROSS THE MIDDLE EAST, bioRxiv, Posted June 24, 2020, doi: https://doi.org/10.1101/2020.06.24.168781

See also...

Armenian confirmation bias

Perhaps a hint of things to come

Understanding the Eneolithic steppe

Maykop ancestry in Copper Age Arslantepe

At least four individuals from the Late Chalcolithic (LC) burial site of Arslantepe show ancestry typical of the population associated with the contemporaneous Maykop culture in the North Caucasus. They are ART018, ART020, ART027 and ART039 from the recent Skourtanioti et al. paper. I've labeled them TUR_Arslantepe_LC_Maykop in my qpAdm mixture model below:

TUR_Arslantepe_LC_Maykop
RUS_Maykop_Novosvobodnaya 0.318±0.041
TUR_Arslantepe_LC 0.682±0.041
chisq 9.969
tail prob 0.533159
Full output

Considering the tight statistical fit, I think it's even possible that some of these people harbor direct ancestry from Maykop Novosvobodnaya. Here's a Principal Component Analysis (PCA) showing why my qpAdm model works so well. It was produced with the data in the text file here and the Vahaduo PCA tools here.

Moreover, one of the Arslantepe males, ART038, belongs to Y-haplogroup R1b-V1636 (R1b1a2). This is clearly a marker of paternal steppe ancestry, because it's been reported in two Eneolithic samples from the southernmost part of the Pontic-Caspian steppe near the North Caucasus foothills (see here). These individuals are dated to ~4,200 calBCE, so they lived about a thousand years earlier than ART038.

ART038 probably lacks steppe and Maykop-related ancestries on his autosomes. Nevertheless, my point about his Y-haplogroup stands, because autosomal admixture can be bred out and disappear completely within a couple hundred years, or about 6 to 8 generations.

Interestingly, Skourtanioti et al. argued against the possibility of significant steppe and Maykop-related ancestries in the Arslantepe LC samples. They also didn't see R1b-V1636 as an obvious signal of paternal steppe ancestry. I find this very puzzling indeed, because to me it seems way off the mark. From the paper:

However, R1b-V1636 and R1b-Z2103 lineages split long before (~17 kya) and therefore there is no direct evidence for an early incursion from the Pontic steppe during the main era of Arslantepe. Lineage L2-L595 found in ALA084 (Alalakh) has previously been reported in one individual from Chalcolithic Northern Iran (Narasimhan et al., 2019) and in three males from the Late Maykop phase in the North Caucasus (Wang et al., 2019). These three share ancestry from the common Anatolian/Iranian ancestry cline described here, which indicates a widespread distribution that also reached the southern margins of the steppe zone north of the Caucasus mountain range.

See also...

Perhaps a hint of things to come

An early Mitanni?

How relevant is Arslantepe to the PIE homeland debate?

An early Mitanni?

I've updated my Global25 datasheets with most of the ancients from the new Skourtanioti et al. paper. Here's a Principal Component Analysis (PCA) based on the data. It was produced with the Vahaduo PCA tools freely available here and the text file here.

Note that one of the Bronze Age females from Alalakh, labeled ALA019, appears to have ancestry from Turan and the Eurasian steppe. She may well have been a Mitanni of Indo-Aryan origin.

Interestingly, a Copper Age male from Arslantepe, ART038, belongs to Y-haplogroup R1b1a2 aka R1b-V1636. This is an unusual find, because R1b hasn't yet been reported in any Copper Age or earlier samples from outside of Europe and the Eurasian steppe.

As far as I can tell, this individual doesn't harbor any genome-wide ancestry from north of the Caucasus. However, R1b-V1636 is a rare lineage that is first attested in Eneolithic samples from the North Caucasus Piedmont steppe, so ART038's Y-chromosome might be the first evidence of the presence of steppe ancestry in Copper Age Anatolia.

I've also added most of the ancients from the new Agranat-Tamir et al. paper to the Gobal25 datasheets. The PCA below is based on the text file available here.

The Megiddo samples include a trio of interesting outliers dated to 1600-1500 BCE with significant ancestry from the steppe. One of these individuals is a male, I2189, who belongs to Y-haplogroup R and probably R1a. So he might also be of Indo-Aryan origin.

Another Megiddo male, S10768, belongs to R1b-M269 and probably shows a few per cent of steppe ancestry. I've already discussed how R1b and steppe ancestry may have ended up in the Bronze Age Near East in a couple of my previous posts:

R1b-M269 in the Bronze Age Levant

How did steppe ancestry spread into the Biblical-era Levant?

R-V1636: Eneolithic steppe > Kura-Araxes?

Did Caucasus hunter-gatherers ever live in what is now Iran?

Nope, they only lived in the Caucasus Mountains. See that's probably why they're called Caucasus hunter-gatherers, or CHG for short.

But what about the hunter-gatherers from the Belt and Hotu caves in northern Iran, you might ask? Well, what about them? They're not CHG, nor are they significantly more CHG-like than the early farmers of the Zagros Mountains.

To illustrate the point, below are a couple of TreeMix graphs. I'd say they're rather straightforward and self-explanatory.

However, please note that I combined the Belt and Hotu individuals into one sample to help keep the marker count at over 100K. Also keep in mind that CHG is represented by Kotias_HG.

See also...

A final note for the year

A note on Steppe Maykop

Did South Caspian hunter-fishers really migrate to Eastern Europe?

Graphing the truth

I haven't used TreeMix since qpGraph became freely available for Linux. Among other things, the latter offers greater control, reproducibility and transparency.

However, I'd say that in its current form qpGraph is not the most objective way to analyze data. That's because if you're really good with it, and you want a graph to work, then often you can make it work by tweaking whatever it is that needs to be tweaked.

It's not possible to do a lot of tweaking with TreeMix. Indeed, once the user picks the samples for the TreeMix run, the rest of the process can be totally unsupervised, and thus free from human interference. Obviously, that's not a guarantee of accuracy, but it can be useful.

I feel I need to run more unsupervised analyses, especially when exploring new data. So to that end, I've dusted off TreeMix and will be using it regularly again.

There's been some talk lately online about migrations from Central Asia giving rise to the Eneolithic populations of the North Caucasus Piedmont steppe. In my opinion, that sounds like nonsense. But let's see what TreeMix has to say on the matter. In the graphs below look for the samples labeled Progress_En and Vonyuchka_En, respectively.

As far as I can tell, both of these graphs essentially corroborate the results from my recent Principal Component Analyses (PCA) with many of the same ancients (see here). In other words, Progress_En and Vonyuchka_En can be described as mixtures of populations closely related to the hunter-gatherers of the Caucasus on one hand, and those of Eastern Europe on the other. How does Central Asia fit into this, you might ask? It doesn't, unless you really want it to.

See also...

Did South Caspian hunter-fishers really migrate to Eastern Europe?

A final note for the year

I feel like I've spent a good part of 2019 banging my head against a thicker than average brick wall.

Much of this feeling is tied to the controversy over the ethnogenesis of the Yamnaya people, and my often futile attempts to explain that their origin cannot be sought in what is now Iran, or, indeed, anywhere outside of Eastern Europe.

This post is my final attempt to lay out the facts in regards to this topic. Next year I'll have better things to do than to argue the bleeding obvious.

Below are two graphs from a Principal Component Analysis (PCA) based on relatively high quality ancient human genotype data from the Caucasus and surrounds. They include two typical Yamnaya individuals from burial sites north of the Caspian Sea. I made the graphs with the Vahaduo Custom PCA tool here. The relevant datasheet can be downloaded here.

Here's what I'm seeing:

- the Yamnaya individuals sit on genetic clines made up of hunter-gatherers native to the Caucasus and various parts of Eastern Europe, including a trio from the southernmost part of the Pontic-Caspian steppe (labeled Steppe_Eneolithic), with whom they form a distinct cluster

- the samples from the Caucasus and the Iranian Plateau form very different clusters, so there's no support here for the ancient Caucasus/Iranian grouping that is often haphazardly invoked in scientific literature

- there's no indication that the Yamnaya and/or Steppe_Eneolithic groups experienced recent gene flow, or, for that matter, any gene flow whatsoever, from what is now Iran.

Of course, analyses based on formal statistics suggest that the Yamnaya population harbors minor western ancestry that is missing in Steppe_Eneolithic. In fact, I was first to argue this point (see here). So let's add a couple of ancient farmers from Western Europe to my PCA to see how they affect the graphs. The relevant datasheet is available here.

Yep, the Yamnaya pair appears to be peeling away very slightly, but deliberately, from the Steppe_Eneolithic individuals towards the part of the plot occupied by the farmers.

Admittedly, I'm no Sherlock Holmes, but even with my fairly average sleuthing abilities, I'm pretty sure I know how the Yamnaya people came to be. They formed largely on the base of a population very much like Steppe_Eneolithic somewhere deep in Eastern Europe, well to the north of the Caucasus, and nowhere near the Iranian Plateau.

See also...

A note on Steppe Maykop

Did South Caspian hunter-fishers really migrate to Eastern Europe?

The idea that most of the Near Eastern-related ancestry in the ancient populations of the Pontic-Caspian (PC) steppe is, one way or another, sourced from the territory of present-day Iran is a fairly popular one nowadays (for instance, see here). It might turn out to be correct, once there are enough relevant samples to test it properly, but in my opinion the chances of this are slim.

My skepticism is based on literally hours of analyses with the currently available ancients from the Caucaso-Caspian region, like, for instance, the admixture graphs below featuring foragers and early farmers from Russia, Georgia and Iran. The relevant qpGraph and dot files are available here.

Note that the further I move away from Eastern Europe in these graphs when looking for the source of the southern ancestry in the Eneolithic population from the southernmost part of the PC steppe (Piedmont_En), the more difficult it is for me to create a statistically sound model. What might this tell us about the provenance of this so called southern ancestry?

See also...

The PIE homeland controversy: August 2019 status report

Some myths die hard

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