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Wednesday, February 27, 2019

The Steppe Maykop enigma

Who were the Steppe Maykop people exactly? Their ancestry must surely rank as one of the biggest surprises served up by ancient DNA to date.

I always thought that they'd turn out roughly like a mixture between populations associated with the Kura-Araxes and Yamnaya cultures (mostly because their territory was located sort of in between them). Nope, that wasn't even close. This is where they cluster compared to Kura-Araxes and Yamnaya samples in my Principal Component Analysis (PCA) of world-wide genetic variation: the Global25.
To explore the ancestry of the Steppe Maykop people in more detail I ran a couple of unsupervised Global25/nMonte tests, using basically every ancient population in the (scaled) Global25 datasheet that seemed chronologically sensible and even remotely relevant. I narrowed things down to these two mixture models.



But, you might say, Global25/nMonte isn't a published analytical method and it doesn't run on formal statistics, the meat and potatoes of ancient DNA papers. OK then, let's try the same models with the qpAdm software, which is a published method and does run on formal statistics, using exactly the same samples.

Geoksiur_Eneolithic 0.100±0.032
Piedmont_Eneolithic 0.433±0.053
West_Siberia_N 0.467±0.028
chisq 19.155
tail prob 0.159096
Full output

Piedmont_Eneolithic 0.429±0.051
Sarazm_Eneolithic 0.119±0.033
West_Siberia_N 0.452±0.026
chisq 18.090
tail prob 0.202699
Full output

They're basically identical. Importantly, my models must reflect reality at some level, because otherwise I wouldn't be able to produce a pair of essentially identical results using such vastly different statistical methods. So the pertinent question is what do these results actually mean?

It seems unlikely to me that we're dealing here with a highly complex three-way mixture process, involving populations from such far flung locations as western Siberia and southern Central Asia. Rather, I suspect that Steppe Maykop was the result of a two-way mixture between Piedmont_Eneolithic (the population that lived before it on the steppe north of the Caucasus) and someone just a little bit more easterly. I'm guessing that the latter was the (as yet unsampled) population associated with the Kelteminar archeological culture.

By the way, please note that Piedmont_Eneolithic is made up of samples from two different locations on the Piedmont steppe, and I occasionally treat them as separate populations labeled Progress_Eneolithic and Vonyuchka_Eneolithic (for instance, see here).

Update 28/02/2019: Below is a PCA focusing on West Eurasian genetic variation. Overall, the position of Steppe Maykop relative to Geoksiur_Eneolithic, Piedmont_Eneolithic and West_Siberia_N appears to reflect my nMonte and qpAdm models. However, as per our discussion in the comments, one of the Steppe Maykop individuals (the most southerly one in the PCA) probably also has recent ancestry from the Caucasus.

See also...

An exceptional burial indeed, but not that of an Indo-European

Maykop: a multi-ethnic layer cake?

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

Saturday, February 23, 2019

Catacomb > Armenia_MLBA

It's now clear, thanks to ancient DNA, that Transcaucasia and surrounds were affected by multiple, and at times significant, population movements from Eastern Europe during the Chalcolithic and Bronze Age periods. Based on the ancient samples from what is now Armenia, I'd say that this process peaked during the Middle Bronze Age. But who exactly were the people who perhaps swarmed south of the Caucasus at this time?

The most likely suspects are the various groups that occupied the southernmost parts of the Pontic-Caspian steppe throughout the Bronze Age. They were associated with the so called Catacomb, Kubano-Tersk and Yamnaya archeological cultures. Below is a Principal Component Analysis (PCA) that compares samples from these cultures with those from Middle to Late Bronze Age Armenia (labeled Armenia_MLBA). The relevant datasheet is available here.

Note that Armenia_MLBA forms a cline that appears to be stretching out towards the Catacomb, Kubano-Tersk, Yamnaya and other Bronze Age steppe groups, and this suggests that it harbors significant and probably recent steppe-related ancestry. But PCA plots based on just two dimensions of genetic variation can be misleading at times, so let's check this out with some formal mixture models using qpAdm.

Catacomb 0.234±0.028
Kura-Araxes_Kaps 0.766±0.028
chisq 10.723
tail prob 0.826248
Full output

Kubano-Tersk 0.254±0.030
Kura-Araxes_Kaps 0.746±0.030
chisq 13.535
tail prob 0.633284
Full output

Kura-Araxes_Kaps 0.768±0.028
Yamnaya_Kalmykia 0.232±0.028
chisq 14.454
tail prob 0.564954
Full output

Kura-Araxes_Kaps 0.762±0.029
Yamnaya_Caucasus 0.238±0.029
chisq 15.916
tail prob 0.458816
Full output

All of these models are statistically very sound, and even though I ranked the results by "tail prob", there's nothing in the output that clearly points to any one of the southern steppe groups as the obvious source of the steppe-related ancestry in Armenia_MLBA. But, interestingly, Catacomb tops the ranking, and it probably also makes the most sense based simply on Carbon-14 chronology. So, for now, I'm going with Catacomb.

I didn't get a chance yet to investigate this issue in detail with the Global25. Does it contradict the results from my PCA and qpAdm analyses? If anyone reading this would like to take a close look that'd be great. Feel free to post your findings in the comments below. And if the answer is indeed Catacomb, then what language did these Catacomb-derived migrants, or perhaps invaders, speak? If not proto-Armenian then what?

By the way, please be aware that the Kubano-Tersk samples in my analyses are the same individuals as those featured in Wang et al. 2019 under the label "North Caucasus".

See also...

Early chariot drivers of Transcaucasia came from...

Likely Yamnaya incursion(s) into Northwestern Iran

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

Sunday, February 17, 2019

On Maykop ancestry in Yamnaya

What Maykop ancestry in Yamnaya? There is none, or at least not enough worth discussing, except in one highly unusual female outlier from a burial in what is now eastern Ukraine. But apparently this is still up for debate? Well it shouldn't be.

To anyone with even a passing interest in the Yamnaya culture, it should be rather obvious that it formed during the tail end of the Eneolithic on the Pontic-Caspian steppe, as basically a direct offshoot of the earlier Repin culture, but perhaps also with significant influences from the earlier still Khvalynsk and Sredny Stog cultures. So why should its population history be much different from this?

It isn't, and this is fairly easy to demonstrate now despite the still rather poor sampling of Eneolithic remains from the Pontic-Caspian steppe.

Below is a series of qpAdm analyses in which I modeled several Yamnaya groups, as well as the closely related Afanasievo and Poltavka populations, exclusively and successfully as two- and three-way mixtures of a few Eneolithic singletons from various parts of the Pontic-Caspian steppe (obviously, I'd love to use homogeneous population sets instead, but, as per my point above, that's not possible yet). The models are sorted by their statistical fits, best to worst. Also note the large number and wide range of right pops or outgroups. I wanted to make sure that I wasn't missing anything.

Dereivka_I_I4110 0.324±0.035
Progress_Eneolithic_PG2004 0.676±0.035
chisq 6.797
tail prob 0.976979
Full output

Progress_Eneolithic_PG2004 0.638±0.038
Sredny_Stog_II_I6561 0.362±0.038
chisq 10.855
tail prob 0.818366
Full output

Progress_Eneolithic_PG2001 0.655±0.073
Sredny_Stog_II_I6561 0.345±0.073
chisq 12.676
tail prob 0.696277
Full output

Dereivka_I_I4110 0.324±0.038
Progress_Eneolithic_PG2004 0.676±0.038
chisq 12.895
tail prob 0.680437
Full output

Khvalynsk_Eneolithic_I0122 0.086±0.054
Sredny_Stog_II_I6561 0.221±0.070
Vonyuchka_Eneolithic_VJ1001 0.693±0.101
chisq 13.113
tail prob 0.593562
Full output

So, you might ask, is there any way to add Maykop to these models? Nope, it's pointless, because it doesn't improve the stats (for instance, see here, here and here). In other words, the situation is this: I already have awesome models, and I can't readily fit Maykop into my framework, so why do it? But if anyone out there wants to try, then by all means, and feel free to share the results with us in the comments.

Of course, the fact that most of these Yamnaya and Yamnaya-related populations are best modeled with somewhat different Eneolithic steppe singletons doesn't mean that they have radically different origins. In fact, they're all very closely related and they're basically like one Bronze Age steppe family. They just harbor somewhat different ratios of the same ancient ancestral components.

For the sake of being thorough, as per scientific literature, I pooled all of the above Afanasievo, Poltavka and Yamnaya samples into a Steppe_EMBA set and analyzed it with several genetically and geographically matching pairs of the Eneolithic singletons. This was one of the best fitting models, which I think is interesting, because the region roughly between the burial sites of these pairs of Eneolithic individuals was the home of the Repin culture.

North_Pontic_Eneolithic_I4110-I656 0.313±0.027
Progress_Eneolithic_PG2001-PG2004 0.687±0.027
chisq 15.378
tail prob 0.497157
Full output

Again, adding Maykop to this model makes no sense (see here, here and here). Clearly, I'd have to come up with a very different framework to successfully model Steppe_EMBA with a Maykop population. However, it's unlikely that such a model would make much sense in the context of various other types of genetic analyses and archeological data.

See also...

Yamnaya: home-grown

Big deal of 2018: Yamnaya not related to Maykop

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

Wednesday, February 13, 2019

Ancient Caucasus open analysis and discussion

The following samples from the recent Wang et al. paper on the genetic prehistory of the Caucasus are now in the Global25 datasheets:

Catacomb MK3003
Catacomb RK4001
Catacomb RK4002
Catacomb SA6003
Darkveti-Meshoko I1722
Darkveti-Meshoko I2055
Darkveti-Meshoko I2056
Kubano-Tersk BU2001
Kubano-Tersk GW1001
Kubano-Tersk LYG001
Kubano-Tersk MK5009
Kubano-Tersk PG2002
Kubano-Tersk RK1003
Kubano-Tersk_Late KBD001
Kubano-Tersk_Late KBD002
Kura-Araxes_Kaps ARM001
Kura-Araxes_Kaps ARM002-003
Kura-Araxes_Velikent VEK007-009
Lola NV3001
Maykop OSS001
Maykop_Late MK5001
Maykop_Late MK5004
Maykop_Late SIJ001
Maykop_Late SIJ002
Maykop_Late SIJ003
Maykop_Novosvobodnaya I6266
Maykop_Novosvobodnaya I6267
Maykop_Novosvobodnaya I6268
Maykop_Novosvobodnaya I6272
North_Caucasus_MBA KDC001
North_Caucasus_MBA KDC002
Progress_Eneolithic PG2001
Progress_Eneolithic PG2004
Steppe_Maykop AY2001
Steppe_Maykop AY2003
Steppe_Maykop SA6001
Steppe_Maykop SA6004
Steppe_Maykop_o IV3002
Steppe_Maykop_o SA6013
Vonyuchka_Eneolithic VJ1001
Yamnaya_Caucasus RK1001
Yamnaya_Caucasus RK1007
Yamnaya_Caucasus SA6010
Yamnaya_Caucasus ZO2002

A lot of people don't seem to be aware of this, but the links are always the same for all of the datasheets, even after major updates:

Global25 datasheet ancient scaled

Global25 pop averages ancient scaled

Global25 datasheet ancient

Global25 pop averages ancient

Feel free to analyze the data in any way you wish and share your findings in the comments. Did the authors miss anything?

See also...

Big deal of 2018: Yamnaya not related to Maykop

Saturday, February 9, 2019

Blast from the past: Matters of basic geography

I'm re-posting this article from 2017 for the benefit of some Science News journalists, who are apparently having major problems dealing with basic geography. That's because they think that the Yamnaya culture was located in Asia rather than Eastern Europe. Take my advice and don't read Science News whatever you do. It might rot your brain.


The steppe north of the Black Sea in Ukraine has basically always been considered a part of Europe, and just over 100 years ago some guy with a map decided that the steppe between the eastern coast of the Black Sea in Russia and the Ural River in western Kazakhstan should also be Europe.

So nowadays, right or wrong, it's generally accepted that the entire steppe region west of the Ural River, known as the Pontic-Caspian steppe, is in Eastern Europe. Here's a map courtesy of Wikipedia showing how the official boundary between Eastern Europe and Asia has shifted since the 18th century.

But this decision wasn't entirely arbitrary, because the current boundary between Eastern Europe and Asia by and large follows several major geographic barriers, including the Caucasus Mountains, the Caspian Sea and the Ural Mountains. It'd be hard to argue that these barriers haven't had a profound impact across the ages on the character of Europe and its people, and this has probably been known for well over a couple hundred years.

For instance, if we're to trust the most common interpretations of the works of ancient geographers like Hecataeus and Herodotus, then their worlds in some important ways resembled the typical Principal Component Analysis (PCA) of West Eurasian genetic variation. And it seems that they had a pretty good idea where both the strong continental boundaries and fuzzy areas were located.

Below, on the geographic map inspired by Herodotus, Europa or Europe is delineated from much of Asia by the Black Sea, the Caucasus Mountains and the Caspian Sea, while on the genetic map, most European and Asian populations form two, more or less parallel, clusters fairly cleanly separated by empty space (this was first noted in Lazaridis et al. 2013). Indeed, this empty space is the work of the Black Sea, the Caucasus Mountains and the Caspian Sea acting as rather effective barriers to gene flow between Eastern Europe and Asia (see Yunusbayev et al. 2012).

However, on the genetic map, the Iranic Scythians of the Asian steppes straddle my somewhat arbitrary red line separating Europa and Asia, and this is echoed on the Herodotus map by Iranic and related peoples like the Massagetae and Issedones, who inhabit the seemingly undefined part of the world between Europa and Asia east of the Caspian Sea (Mare Caspium).

Nothing really ground breaking, but pretty cool stuff.

On a related note, I've seen the term "mainland Europe" used recently in at least one of the big ancient DNA papers to describe the part of Europe west of the Pontic-Caspian steppe. It seems that the authors wanted to underline the fairly stark genetic difference that existed between most of Europe and the steppe just prior to the expansion of Yamnaya and related steppe herder groups that initiated the formation of the present-day European gene pool.

I can see why they did this, but to my mind they got things backwards. That's because the term mainland implies the opposite of island and/or peninsula, and of course the part of Europe west of the Pontic-Caspian steppe is a relatively narrow strip of land surrounded by water, so it's a peninsula. Let's visualize these two models on a map of Europe courtesy of Wikipedia:

I understand that my model might result in heart palpitations for some readers, especially those from Western Europe, who generally see their part of Europe as core Europe, but I feel that it makes good sense from a purely geographic POV.

See also...

Max Planck scientists: on a mission against geography

Genetic borders are usually linguistic borders too

Thursday, February 7, 2019

A Bell Beaker superhighway

Below is a density heat map of Bell Beaker pottery finds from a recent paper titled Der Glockenbecher in Europa - eine Karteirung (The mapping of the Bell Beaker in Europe). It's freely available as part of a series of new archeological papers on the Bell Beaker phenomenon at the Journal of Neolithic Archeology (see here).

Particularly eye catching, at least for me, is the trail of high density clusters that runs from the Carpathian Basin to the North Sea, especially in the context of recent online discussions about the potential geographic origins of the non-Iberian, or Yamnaya-related, Beakers with significant steppe ancestry. I'm guessing that this was something of a Beaker superhighway back in the day.

By itself, the heat map is probably very favorable to the rather popular idea nowadays that the Yamnaya-related Beakers originated in the Carpathian Basin. Their ancestors, for instance, may have been Yamnaya groups that arrived from the Pontic-Caspian steppe via the Balkans, and their ethnogenesis may have been sparked by the cultural impulses that were streaming into the region from across Europe, perhaps from as far away as Iberia. The descendants of these early, potentially Yamnaya-derived, Beakers may then have moved en masse to the North Sea region and beyond via the aforementioned superhighway.

However, fortunately, we now also have quite a bit of ancient DNA data to throw into such debates. Note that I added the following labels to the map: Beaker The Netherlands, Beaker Mittelelbe-Saale, Beaker Bohemia, and Beaker Hungary. These are the currently sampled Beaker populations from along the so called superhighway, and you can see how they cluster compared to each other in my Principal Component Analysis (PCA) of ancient West Eurasian genetic variation.

Clearly, what we're dealing with here is not just a series of well settled sites, or a heavily populated trade route, but also a busy migration trail, because of the significant overlap in the PCA between almost all of the Beaker populations.

Interestingly, though, most of the gene flow appears to have gone from the northwest to the southeast, because the Dutch Beakers hardly overlap with the other groups, and arguably form the tightest cluster, suggesting that they're the most genetically homogeneous and unadmixed of these Beakers. Indeed, they're also genetically very similar to the earlier nearby Corded Ware groups from Germany and Scandinavia, so it's unlikely that they derive from recent migrants to Northern Europe. On the other hand, the Hungarian Beakers from the Carpathian Basin are by far the most dispersed of the lot, which certainly means that they're the least genetically homogeneous and probably the most admixed.

Note also that some of them do clearly "pull" towards the Dutch Beakers, suggesting that they might harbor significant ancestry from as far north as the shores of the North Sea.

See also...

The Boscombe Bowmen

Single Grave > Bell Beakers

Dutch Beakers: like no other Beakers

Monday, February 4, 2019

The tracer dye

Remember that Wang et al. preprint at bioRxiv on the genetic prehistory of the Greater Caucasus? Well, it's just been published at Nature Communications under a new title: Ancient human genome-wide data from a 3000-year interval in the Caucasus corresponds with eco-geographic regions.

The authors also re-worked a few other parts of the manuscript, including the abstract and figures, but most of it looks pretty much the same as the bioRxiv version from May 2018. It's hard for me to believe that this process took more than half a year, so I'm guessing this is just how long it takes sometimes to get a paper into this journal.

In any case, the supplementary information includes a Peer Review File (see here) with a couple of interesting comments in regards to the Proto-Indo-European (PIE) homeland debate. Emphasis is mine:

Reviewer no 2: This hypothesis about the Caucasus source of Proto-Indo-European has been advanced also for slightly other reasons by David Reich and Kristian Kristiansen, so I think it should be elaborated here by the authors and they should marshall their new results to add whatever support they can. However, this hypothesis should rest on showing a sustained admixture between Maikop and Yamnaya to serve as a bridge to Yamnaya from the Caucasus (because the authors accept Yamnaya as connected to later PIE.) It is difficult to see in the results presented here a sustained gene flow from Maikop into Yamnaya, that would sustain this hypothesis. On lines 410 and 432 the authors preferred to see the Anatolian Farmer genes that appeared in Yamnaya as flowing from southeastern Europe, with a 20% WHG component, not from Maikop, without the WHG component. If most of the c. 15% Anatolian Farmer found in Yamnaya came from the west, it leaves very little room for gene flow into Yamnaya from Maikop. If the 3% WHG that makes the difference between a western and Caucasian source of Anatolian Farmer is strongly supported by their data, that makes a Caucasian origin of PIE less likely because it reduces gene flow from Maikop into the steppes. In fact it suggests that very little south-to-north gene flow occurred during the Maikop period (except into 2 individuals from a distinct, small, local genetic group different from Maikop and Yamnaya). This is puzzling and unexpected, but also it fails to support the bridge that seems to be needed.

Reply: We’re afraid that this might be a misunderstanding. There is indeed very limited gene flow between the Caucasus and the steppe groups (apart from the examples highlighted). However, we have based our PIE-related speculations on the observation that the CHG/Iranian (green) ancestry component is increasing already during the Eneolithic north of the Caucasus. This led us to propose that this might be the actual ‘tracer dye’ of an early PIE spread, which could then also accommodate the spread of PIE south of the mountain range where this ancestry component also rises in frequency resulting in a relatively homogenised dual ancestry (Anatolian + Iranian farming-related ancestry) in Chalcolithic times (see also brown arrow in Figure 2).

A misunderstanding? Perhaps, but my impression from reading both the preprint and paper was that the authors really wanted Maykop to be the source of Indo-European languages on the Pontic-Caspian steppe, even if they didn't spell this out explicitly. So I'm not surprised by the peer reviewer's line of inquiry.

I think what actually happened was that the authors got it in their heads long ago that the PIE homeland was south of the Caucasus, simply because that's what they saw when they looked at the spread, across space and time, of some exceedingly broad and very ancient genome-wide genetic components, especially one such component with roots in the Caucasus and surrounds that was found both in Yamnaya and Hittite samples. And they penciled in Maykop, probably because of archeological data, as the most likely vector for the spread of this potential PIE "tracer dye" onto the steppe.

But obviously that didn't work out once they had a good look at their ancient DNA from the Caucasus, and it seems that they couldn't come up with a coherent alternative theory. Little wonder, considering that their ancient DNA showed a profound genetic differentiation between the Eneolithic/Bronze Age populations of the Caucasus and the Pontic-Caspian steppe, especially in terms of paternal ancestry, which is crucial in linguistics debates.

Whatever. I've already said way too much on this topic, so I'm now moving on. But I'm certainly looking forward to the genotype data from this paper. Analyzing it is going to be a hoot.

See also...

PIE Urheimat poll: two or three options left

Big deal of 2018: Yamnaya not related to Maykop

R-V1636: Eneolithic steppe > Kura-Araxes?

Friday, February 1, 2019

The Boscombe Bowmen

I'm thinking that the Boscombe Bowmen site in Wiltshire, southern England, might be a valuable case study of how the Bell Beaker population, and thus also the present-day western European gene pool, came to be.

Dated to 2500–2140 BCE, this isn't an especially early Bell Beaker grave, but its inventory is intriguing. It includes seven All-Over-Cord (AOC) beakers and one Cord-Zoned-Maritime (CZM) beaker.

Maritime beakers are quintessential Bell Beaker gear, and they're named as such because most of them have been recovered from sites along the Atlantic and Mediterranean coasts. However, strictly speaking, AOC beakers aren't Bell Beaker artifacts. Rather, their origin is said to be in the Single Grave culture, which is, of course, the northwestern European variant of the Corded Ware culture.

Genotype data for two samples from the Boscombe cemetery were analyzed in and published along with last year's Olalde et al. Beaker paper. In tune with the archeological data, one of these individuals came out very Corded Ware-like, with a lot of steppe ancestry, and the other rather southern, with among the lowest level of steppe ancestry for a Beaker dated to later than ~2500 BCE.

To take a closer look at their genetic affinities, I put together the graph below based on a couple of D-stats of the form D(Mbuti,X)(Yamnaya_Samara)/D(Mbuti,X)(Barcin_N,WHG). The bowmen are labeled I2416 and I2417, and the relevant datasheet is available here.

Considering these results, I2416 and I2417 may have been migrants, or the descendants of migrants, from such relatively far flung places as, say, what are now northern Germany and western France, respectively. [Edit: as per the comments below, these individuals are probably third-degree relatives, which makes it unlikely that they're migrants to the region, although it's still possible that their recent ancestors may have been migrants]

Note also that almost all of the populations are basically sitting between the two bowmen. This indeed suggests to me that the cultural processes and resulting population mixtures that took place at the Boscombe site also played out across the width and breadth of the Beaker realm, giving rise to heterogeneous Beaker groups almost everywhere within it and, eventually, the present-day western European gene pool.

Most of the Scandinavians, as well as the closely related British Anglo-Saxons, are slightly pulled above the red trend line by their excess genetic affinity to Western European Hunter-Gatherers (WHG). This phenomenon appears to date back to at least 2275-2032 BCE, because Nordic_LN:RISE98 is clearly affected by it and dated to this period.

My guess is that Single Grave populations from what is now Denmark and surrounds harbored much higher levels of WHG-related ancestry than the more easterly Corded Ware (aka Battle-Axe) Scandinavian groups, and they passed this onto present-day Scandinavians. Nordic_LN:RISE98, although from a burial site in what is now southern Sweden, might well be of Danish Single Grave origin.

See also...

Single Grave > Bell Beakers

Dutch Beakers: like no other Beakers

Hungarian Yamnaya > Bell Beakers?