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Thursday, March 21, 2019

Ancient island hopping in the western Mediterranean (Fernandes et al. 2019 preprint)


Over at bioRxiv at this LINK. Here's the abstract, emphasis is mine:
A series of studies have documented how Steppe pastoralist-related ancestry reached central Europe by at least 2500 BCE, while Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BCE. However, the spread of these ancestries into the western Mediterranean where they have contributed to many populations living today remains poorly understood. We generated genome-wide ancient DNA from the Balearic Islands, Sicily, and Sardinia, increasing the number of individuals with reported data from these islands from 3 to 52. We obtained data from the oldest skeleton excavated from the Balearic islands (dating to ~2400 BCE), and show that this individual had substantial Steppe pastoralist-derived ancestry; however, later Balearic individuals had less Steppe heritage reflecting geographic heterogeneity or immigration from groups with more European first farmer-related ancestry. In Sicily, Steppe pastoralist ancestry arrived by ~2200 BCE and likely came at least in part from Spain as it was associated with Iberian-specific Y chromosomes. In Sicily, Iranian-related ancestry also arrived by the Middle Bronze Age, thus revealing that this ancestry type, which was ubiquitous in the Aegean by this time, also spread further west prior to the classical period of Greek expansion. In Sardinia, we find no evidence of either eastern ancestry type in the Nuragic Bronze Age, but show that Iranian-related ancestry arrived by at least ~300 BCE and Steppe ancestry arrived by ~300 CE, joined at that time or later by North African ancestry. These results falsify the view that the people of Sardinia are isolated descendants of Europe's first farmers. Instead, our results show that the island's admixture history since the Bronze Age is as complex as that in many other parts of Europe.


Fernandes et al., The Arrival of Steppe and Iranian Related Ancestry in the Islands of the Western Mediterranean, bioRxiv, posted March 21, 2019, doi: https://doi.org/10.1101/584714

Update: Another preprint on a similar theme by Marcus et al. has appeared at bioRxiv (see here).

Abstract: Recent ancient DNA studies of western Eurasia have revealed a dynamic history of admixture, with evidence for major migrations during the Neolithic and Bronze Age. The population of the Mediterranean island of Sardinia has been notable in these studies -- Neolithic individuals from mainland Europe cluster more closely with Sardinian individuals than with all other present-day Europeans. The current model to explain this result is that Sardinia received an initial influx of Neolithic ancestry and then remained relatively isolated from expansions in the later Neolithic and Bronze Age that took place in continental Europe. To test this model, we generated genome-wide capture data (approximately 1.2 million variants) for 43 ancient Sardinian individuals spanning the Neolithic through the Bronze Age, including individuals from Sardinia's Nuragic culture, which is known for the construction of numerous large stone towers throughout the island. We analyze these new samples in the context of previously generated genome-wide ancient DNA data from 972 ancient individuals across western Eurasia and whole-genome sequence data from approximately 1,500 modern individuals from Sardinia. The ancient Sardinian individuals show a strong affinity to western Mediterranean Neolithic populations and we infer a high degree of genetic continuity on the island from the Neolithic (around fifth millennium BCE) through the Nuragic period (second millennium BCE). In particular, during the Bronze Age in Sardinia, we do not find significant levels of the "Steppe" ancestry that was spreading in many other parts of Europe at that time. We also characterize subsequent genetic influx between the Nuragic period and the present. We detect novel, modest signals of admixture between 1,000 BCE and present-day, from ancestry sources in the eastern and northern Mediterranean. Within Sardinia, we confirm that populations from the more geographically isolated mountainous provinces have experienced elevated levels of genetic drift and that northern and southwestern regions of the island received more gene flow from outside Sardinia. Overall, our genetic analysis sheds new light on the origin of Neolithic settlement on Sardinia, reinforces models of genetic continuity on the island, and provides enhanced power to detect post-Bronze-Age gene flow. Together, these findings offer a refined demographic model for future medical genetic studies in Sardinia.

Marcus et al., Population history from the Neolithic to present on the Mediterranean island of Sardinia: An ancient DNA perspective, bioRxiv, posted March 21, 2019, doi: https://doi.org/10.1101/583104

See also...

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

Monday, March 18, 2019

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


I was going to write a huge post on the linguistic implications of the latest batch of ancient DNA from Iberia courtesy of Olalde et al. 2019, and then I thought better of it. Admittedly, I don't know enough about the languages of prehistoric Iberia to say anything really useful on the topic. So instead here's an open thread to bounce around a few ideas in the comments.

Just briefly, this is what Olalde et al. say in the abstract of their paper about the relationship between ancestry from the Pontic-Caspian steppe and languages in Iron Age Iberia:

We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia’s ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European–speaking regions but also into non Indo-European–speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia.

However, in the paper it's revealed that "Indo-European regions" actually refers to a Celtic-speaking part of northern Iberia. And it's quite possible that Celts moved into this area from outside of Iberia only during the Iron Age. In other words, the speakers of Indo-European languages here may not have been the descendants of any of the people with steppe ancestry who came to Iberia by ~2000 BCE.

So I'm probably not alone in thinking that the question of the linguistic affinities of these early migrants with steppe ancestry to Iberia (mostly associated with the Bell Beaker culture or BBC) remains open, especially since they evidently had such a profound genetic impact on the later non Indo-European-speaking populations of southern Iberia. Could they have been the speakers of unattested Indo-European languages, as well as Proto-Iberian and Proto-Basque? If not, why not?

Below is a Principal Component Analysis (PCA) of West Eurasian genetic variation. I highlighted some of the ancient samples from Olalde et al., as well as Basques and other present-day Iberians. The Basques form a tight cluster with most of the Copper, Bronze and Iron Age Iberians, and, unlike the other present-day Iberians, they basically look like an Iberian population from the metal ages. The relevant datasheet is available here.


This is nothing new and very much in line with the results in Olalde et al., but I wanted to emphasize the point that Basques were not just a group that experienced an extreme founder effect in R1b-P312, which is a Beaker-specific Y-chromosome lineage. Rather, they're still very similar to Iberian Beakers in terms of overall genetic structure. So where did they get their language?

See also...

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

Saturday, March 16, 2019

Let's try a formal heuristic approach


I created a massive outgroup f3-statistics matrix, featuring almost 300 ancient and present-day populations and individuals, for the purpose of running unsupervised, or at least semi-supervised, fine scale mixture tests with nMonte. Most of the stats were computed with 400-900K SNPs, which is a lot and should provide plenty of power. The matrix is available in a zip file here.

The results I'm getting with this new setup are very similar to those obtained with the Global25. The main differences, as far as I can see for now, are that the f3 data produce more stable results when modeling very deep ancestry, while the Global25 provides more accuracy when modeling fine scale recent ancestry (probably because it's better at picking up more recent genetic drift).

Let's investigate some pertinent issues with the new data using nMonte and PAST. How about we start with these?

- where did Bell Beakers get their steppe ancestry from?

- which Steppe_MLBA group did Indians get their steppe ancestry from?

- do the present-day Irish have any Hallstatt ancestry?

- what is the origin of present-day Basques?

- what is the precise ancestry of Armenia_ChL?

- do the Swat Iron Age samples really lack BMAC ancestry?

- does Anatolia_MLBA really lack steppe ancestry?

Note that the f3 matrix includes the ancients from the new Olalde et al. paper on the genomic history of Iberia (see here). I've also updated the Global25 datasheets with most of these samples.

Global 25 datasheet (scaled)

Global 25 pop averages (scaled)

Global 25 datasheet

Global 25 pop averages

By the way, Hajji_Firuz_ChL I2327, from Narasimhan et al. 2018, is now labeled Hajji_Firuz_IA in the above datasheets, because my understanding is that he's actually from the Iron Age rather than the Chalcolithic period. For background reading about this controversial sample see here and here. I don't have any more info on this topic; we'll just have to wait for the formal publication of the Narasimhan et al. manuscript to get all the details. Apparently it's coming very soon.

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...

Thursday, March 14, 2019

Two new papers on ancient Iberia


Olalde et al. 2019 (Science) at this LINK...

Abstract: We assembled genome-wide data from 271 ancient Iberians, of whom 176 are from the largely unsampled period after 2000 BCE, thereby providing a high-resolution time transect of the Iberian Peninsula. We document high genetic substructure between northwestern and southeastern hunter-gatherers before the spread of farming. We reveal sporadic contacts between Iberia and North Africa by ~2500 BCE and, by ~2000 BCE, the replacement of 40% of Iberia’s ancestry and nearly 100% of its Y-chromosomes by people with Steppe ancestry. We show that, in the Iron Age, Steppe ancestry had spread not only into Indo-European–speaking regions but also into non-Indo-European–speaking ones, and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia. Additionally, we document how, beginning at least in the Roman period, the ancestry of the peninsula was transformed by gene flow from North Africa and the eastern Mediterranean. DOI: 10.1126/science.aav4040

Villalba-Mouco et al. 2019 (Current Biology) at this LINK...

Summary: The Iberian Peninsula in southwestern Europe represents an important test case for the study of human population movements during prehistoric periods. During the Last Glacial Maximum (LGM), the peninsula formed a periglacial refugium [1] for hunter-gatherers (HGs) and thus served as a potential source for the re-peopling of northern latitudes [2]. The post-LGM genetic signature was previously described as a cline from Western HG (WHG) to Eastern HG (EHG), further shaped by later Holocene expansions from the Near East and the North Pontic steppes [3, 4, 5, 6, 7, 8, 9]. Western and central Europe were dominated by ancestry associated with the ∼14,000-year-old individual from Villabruna, Italy, which had largely replaced earlier genetic ancestry, represented by 19,000–15,000-year-old individuals associated with the Magdalenian culture [2]. However, little is known about the genetic diversity in southern European refugia, the presence of distinct genetic clusters, and correspondence with geography. Here, we report new genome-wide data from 11 HGs and Neolithic individuals that highlight the late survival of Paleolithic ancestry in Iberia, reported previously in Magdalenian-associated individuals. We show that all Iberian HGs, including the oldest, a ∼19,000-year-old individual from El Mirón in Spain, carry dual ancestry from both Villabruna and the Magdalenian-related individuals. Thus, our results suggest an early connection between two potential refugia, resulting in a genetic ancestry that survived in later Iberian HGs. Our new genomic data from Iberian Early and Middle Neolithic individuals show that the dual Iberian HG genomic legacy pertains in the peninsula, suggesting that expanding farmers mixed with local HGs. DOI:https://doi.org/10.1016/j.cub.2019.02.006

See also...

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

Single Grave > Bell Beakers

CHG or no CHG in Bronze Age western Iberia?

Thursday, March 7, 2019

A challenge


The datasheets below contain outgroup f3-statistics for a wide range of ancient and present-day populations. Five of the ancient groups and individuals are labeled "Unknown". In fact, I do know what they are, but I'd like you to try and work out whether they were the speakers of Indo-European or non-Indo-European languages by analyzing the datasheets with, say, PAST or nMonte.

f3-stats_language_challenge1.dat

f3-stats_language_challenge2.dat

I'll reveal the identities and likely languages of the mystery ancients in a couple of days. It'll be interesting to see if any of you nail this challenge. It shouldn't be too difficult, but to help things along, I color coded the populations in the datasheets (black = Indo-European, blue = Uralic, and grey = neither). If you haven't done this sort of thing before, these blog posts might be useful as background reading.

Maykop: a multi-ethnic layer cake?

Global25 PAST-compatible datasheets

D-stats/nMonte open thread

Update 09/03/2019: Samuel nailed the challenge in the first post below. And then Matt almost figured out the precise identities of the mystery ancients here. In hindsight I should've made this more difficult. Here are the answers:

Unknown1 = England_Anglo-Saxon (Indo-European) > more here
Unknown2 = Levanluhta_IA (non-Indo-European) > more here
Unknown3 = Minoan_Lasithi (non-Indo-European) > more here
Unknown4 = Slavic_Bohemia (Indo-European) > more here
Unknown5 = Turkmenistan_IA (Indo-European) > more here

Monday, March 4, 2019

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


Not too many people have been buried sitting on wagons. The most famous case is that of an Early Bronze Age man who, considering his injuries, may have died in a high-speed crash - high-speed for its time anyway - on the Pontic-Caspian steppe in Eastern Europe.

It's likely that this guy was one of the very first wagon-drivers in human history, because his four-wheeled wooden model is dated to 3336-3105 calBCE, which makes it the oldest wagon discovered thus far. His genotype data, under the label Steppe Maykop SA6004, were published recently along with Wang et al. 2019.

Early wagons are very important for a couple of reasons: they revolutionized human transport and warfare, and they're often closely associated with the prehistoric expansions of Indo-European languages.

So I'm pretty sure that many of you must be thinking right now that wagon-driver SA6004 was an early Indo-European, or even a Proto-Indo-European! I bet that's what Wang et al. thought too, considering the conclusion in their paper. But, alas, the chances of this are slim to none.

Steppe Maykop samples show rather peculiar genetic structure considering their geographic origin, with a large proportion of their ancestry deriving from a source closely related to western Siberian hunter-gatherers (aka West_Siberia_N in the ancient DNA record). Indeed, SA6004 basically looks like a 50/50 mix between West_Siberia_N and Piedmont_Eneolithic. Here's a map with all of the relevant details.


Thus, clearly, the Steppe Maykop population wasn't ancestral or even directly related to the steppe and steppe-derived groups generally regarded to have been Indo-European speaking, such as those associated with the Yamnaya, Corded Ware, and Bell Beaker cultures. That's because these groups lack any discernible West_Siberia_N-related ancestry.

It also wasn't ancestral or directly related to any present-day or currently sampled ancient Indo-European speaking populations, again because these populations basically lack West_Siberia_N-related ancestry.

On the other hand, Yamnaya, Corded Ware and other closely related groups show an exceptionally strong genetic relationship with Indo-European speakers, especially those from across Northern Europe, which experienced massive migrations from the Pontic-Caspian steppe during the late Neolithic period, and hardly anything from elsewhere since then.

Case in point, the samples from Wang et al. labeled Yamnaya Caucasus were recovered from the same area of the Pontic-Caspian as their Steppe Maykop samples, and yet, take a look at this linear model based on outgroup f3-statistics. Steppe Maykop does show high genetic affinity to Indo-European speakers (no doubt mediated via its Piedmont_Eneolithic-related ancestry), but, unlike Yamnaya Caucasus, it also shows unusually high affinity for a West Eurasian population to Native Americans and Siberians. The relevant datasheet is available here.
So the only way that the Steppe Maykop population was Indo-European-speaking, was if it inherited its Indo-European speech from its Piedmont_Eneolithic-related ancestors. And even if it was Indo-European-speaking, it probably spoke an extinct Indo-European language not closely related to any extant Indo-European languages. In other words, the possibility that Steppe Maykop passed on its language to Yamnaya, along with its wagons, is close to zero. More likely, Yamnaya stole a few wagons from Steppe Maykop, and the rest is history.

See also...

The Steppe Maykop enigma

On Maykop ancestry in Yamnaya

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

Saturday, March 2, 2019

Maykop: a multi-ethnic layer cake?


Let's speculate about the linguistic affinities of the currently available ancient populations from the Caucasus and surrounds. I put together a series of outgroup f3-stats to help things along. They're available for download here.

Maykop
Georgian 0.258224
Abkhasian 0.257899
Latvian 0.257376
Swedish 0.257301
Turkish_Trabzon 0.256996
Basque_Spanish 0.256589
Chechen 0.256514
Icelandic 0.256418
Norwegian 0.256325
Lezgin 0.256272
Irish 0.256227
Tabasaran 0.256092
Italian_Bergamo 0.25605
English_Cornwall 0.256032
Polish_East 0.255991
Scottish 0.255955
Adygei 0.255913

Steppe_Maykop
Latvian 0.261845
Russian_North 0.26145
Estonian 0.260355
Finnish 0.260211
Lithuanian 0.260072
Udmurd 0.259804
Ingrian 0.259663
Surui 0.259637
Vepsa 0.259608
Karelian 0.259532
Karitiana 0.259482
Russian_West 0.259397
Russian_Central 0.259274
Wichi 0.259106
Saami 0.258982
Komi 0.258945
Icelandic 0.258854
Swedish 0.258814
Mordovian 0.258604
Irish 0.25859

Eyeballing the stats might be enough to get a general impression about what they mean, but to understand them properly it's necessary to get technical with something like PAST3 (see here). That's because f3-stats pick up shared genetic drift from all drift paths, and don't especially focus on more recently shared ancestry. This can often lead to confusing outcomes.

Below are a few examples of linear models based on my f3-stats. Note that many Indo-European speakers, especially from Northern Europe, are foremost attracted to ancient samples from the Pontic-Caspian steppe. On the other hand, non-Indo-European speakers, from such far flung locations as the Caucasus and Iberia, show relatively stronger affinity to ancient samples from Anatolia and the Caucasus. Moreover, Uralic speakers show elevated affinity to ancient hunter-gatherer samples from Eastern Europe and Siberia. Makes sense, right?
Based on these and other data, I'd say that Maykop and the culturally related Steppe Maykop were something of a multi-ethnic polity, with many near and far related languages spoken by its people, including perhaps Kartvelian, Northwest Caucasian, Yeniseian and Indo-European. But it seems to me that Proto-Indo-European was spoken by steppe foragers turned pastoralists just outside of the Maykop zone. And I'm quite sure that after the Maykop collapse various early Indo-European groups pushed across the Caucasus and deep into the Near East. Just take a look at the f3-stats and linear model for Hajji_Firuz_BA to see what I mean.

See also...

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

The Steppe Maykop enigma

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

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.

Steppe_Maykop
Geoksiur_Eneolithic,11.2
Piedmont_Eneolithic,44.4
West_Siberia_N,44.4
distance%=1.5161

Steppe_Maykop
Piedmont_Eneolithic,46.6
Sarazm_Eneolithic,10.4
West_Siberia_N,43
distance%=1.6408

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.

Steppe_Maykop
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

Steppe_Maykop
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...

Monday, February 25, 2019

All quiet on the eastern front


I put together this quick and dirty qpGraph tree just to double check what the Eneolithic trio from the Piedmont steppe (Piedmont_Eneolithic) were roughly made of, and how they related to some of the other populations from the eastern half of ancient West Eurasia. The relevant graph file is available here.


Yep, the tree basically lines up with scientific literature. In other words, Piedmont_Eneolithic appears to be a two-way mixture of populations very closely related to Caucasus and Eastern European Hunter-Gatherers (CHG and EHG, respectively). Good to know.

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 new version of the tree designed specifically to investigate whether the ancestry of Piedmont_Eneolithic can be modeled with admixture from Darkveti-Meshoko, a population from the Caucasus roughly contemporaneous with Piedmont_Eneolithic. This doesn't appear to be the case, at least not with this topology, because the mixture edge from the Darkveti-Meshoko-related D7 node to the Piedmont_Eneolithic-related E4 node is marked with a zero. The relevant graph file is available here.


See also...

Big deal of 2018: Yamnaya not related to Maykop

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

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.

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

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

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

Armenia_MLBA
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".

On a related note, here are a couple of intriguing qpAdm models that I came up with recently for the five Hittite era Anatolians in my dataset (aka Anatolia_MLBA). I don't have a clue why these models work so well and what they mean exactly. They do suggest, however, that the Hittite era Anatolians harbor steppe-related ancestry, which may have been mediated via populations from the Caucasus similar to Armenia_MBA. But, then again, this might just be an artifact of trying to model several streams of ancestry, coming from various directions, with just two and three potential mixture sources. Any thoughts?

Anatolia_MLBA
Anatolia_EBA_Ovaoren 0.651±0.109
Armenia_MBA 0.174±0.063
Peloponnese_N 0.175±0.058
chisq 8.321
tail prob 0.91027
Full output

Anatolia_MLBA
Anatolia_EBA_Isparta 0.831±0.053
Armenia_MBA 0.169±0.053
chisq 16.170
tail prob 0.441163
Full output

See also...

Steppe ancestry in Chalcolithic Transcaucasia (aka Armenia_ChL explained)

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.

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

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

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

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

Yamnaya_Caucasus
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.

Steppe_EMBA
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:

Global 25 datasheet (scaled)

Global 25 pop averages (scaled)

Global 25 datasheet

Global 25 pop averages

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 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 as 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?

Tuesday, January 22, 2019

Hungarian Yamnaya predictions


About ten thousand ancient burial mounds still stand in the Carpathian Basin and surrounds. Many of these kurgans or tumuli show direct archeological links with the highly mobile Yamnaya culture of the Pontic-Caspian steppe to the east, and may have been built by Yamnaya migrants.

The testing of ancient DNA from the remains in these burials is important, because the results are likely to be informative about the profound genetic, cultural and linguistic changes that took place in what is now Hungary and the Balkans during the Copper and Bronze Ages.

But, alas, probably to the disappointment of some readers, my great prediction is that they're not going to be overly relevant to what happened at this time in Northern and Western Europe, and won't upend the current consensus that the Corded Ware culture (CWC) was the main vector for the spread of steppe ancestry and Indo-European languages into these parts of the continent.

The important thing to understand about the Yamnaya expansion into the Carpathian Basin is that it mostly stopped at the Tisza River. It's true that some archeological cultures west of the Tisza, such as Mako and Vucedol, do show fairly strong Yamnaya influences, but they can't be regarded as part of the Yamnaya colonization of Central Europe. Below is a slightly modified map from Heyd 2011 to illustrate my point.


In fact, four early Yamnaya period samples from one of the few kurgans west of the Tisza have already been published along with the Olalde et al. 2018 paper on the Bell Beaker culture (BBC). And one of these samples, labeled I5117, even represents a male buried in a Yamnaya-like pose. But this is how three of these individuals cluster in my Principal Component Analysis (PCA) of ancient West Eurasian genetic variation.


They sit firmly among other Copper Age and Neolithic samples from west of the Pontic-Caspian steppe. In other words, they show practically zero Yamnaya-related or steppe ancestry. Moreover, both of the males belong to Y-haplogroup G2a-L91, which is yet to be found in any samples from the Copper and Bronze Age steppe.

That's not to suggest, however, that the spread of the Yamnaya culture into the Carpathian Basin was a cultural process with little or no genetic impact. It probably wasn't, because five samples labeled "Yamnaya Hungary" were featured in the Wang et al. 2018 preprint on the genetic prehistory of the Greater Caucasus, and judging by their PCA and ADMIXTURE results (in the figure below from the said preprint) they're not very different from most Yamnaya samples, such as those from far to the east in Kalmykia or Samara.


But the point I'm making is that not every one of the ten thousand kurgans and tumuli in the Carpathian Basin and surrounds was built by newcomers from the steppe, and, thus, my other prediction is that a fair proportion of the Yamnaya-related burial mounds, especially west of the Tisza, might contain remains without any steppe ancestry.

As far as I know, the Y-haplogroups of the aforementioned Yamnaya Hungary samples haven't yet been reported anywhere. But there are three ancients in the Mathieson et al. 2018 paper on the genetic prehistory of southeastern Europe that are probably highly informative about what we can expect in this context, because based on their archeology and ancestry, they're likely to be closely related to the Hungarian Yamnaya population. They are:

Balkans_BronzeAge I2165: Y-hg I2a-L699 3020-2895 calBCE

Vucedol_Croatia I3499: Y-hg R1b-Z2103 2884-2666 calBCE

Yamnaya_Bulgaria Bul4: Y-hg I2a-L699 3012-2900 calBCE

That's not much to work with, you might say. Perhaps, but keep in mind that R1b-Z2103 has now been reported in Yamnaya samples from Ciscaucasia, Kalmykia, and Samara, while I2a-L699 in a Yamnaya singleton from Kalmykia. Thus, a lot of outcomes are still possible, but some are more likely than others. So I'm expecting most Hungarian Yamnaya males to belong to R1b-Z2103 and I2a-L699, or perhaps even the other way around!

However, in line with my great prediction, I don't expect to see any R1a-M417 or R1b-L51, the two most common Y-halogroups among present-day Europeans living north and west of the Balkans. And I think that if these markers do actually show up, then they'll be represented by nowadays rare or even extinct lineages that aren't very important to the peopling of Europe. Any thoughts? Feel free to share them in the comments.

See also...

Hungarian Yamnaya > Bell Beakers?

Single Grave > Bell Beakers

Dutch Beakers: like no other Beakers

Saturday, January 19, 2019

Dutch Beakers: like no other Beakers


In my last two blog posts I tried to explain why the so called Bell Beakers of prehistoric Europe cannot be confidently derived in any significant way from the Yamnaya population of the Carpathian Basin, and are more likely to have been an offshoot, in varying degrees, of the Single Grave or Corded Ware people of the Lower Rhine region (see here and here).

To help drive my message home, below is a series of new Principal Component Analysis (PCA) plots that illustrate the unique position of Dutch Beakers from the Lower Rhine relative to the Corded Ware population of Germany and all the other Beaker groups sampled to date. The relevant datasheet is available here.

The Dutch Beakers don't exactly sit between the Corded Ware and the other Beaker samples, but generally at the apex of their clusters, suggesting to me that they're not a mixture between Corded Ware and one or more of the other Beaker groups, but rather, as per my recent argumentation, a genetically homogeneous, relatively unique and thus long-standing Corded Ware-related population that may have contributed significant gene flow to the other Beaker groups.

Please note also that all of these outcomes can be confirmed with various types of formal statistics. I know this because I've done it.


See also...

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

Wednesday, January 16, 2019

Single Grave > Bell Beakers


I've been studying in detail the genetic substructures within the Bell Beaker population with formal statistics and Principal Component Analyses (PCA). As far as I can see, among the two most homogeneous, and thus least likely to be recently admixed, Beaker groups are the Dutch Beakers and also the Dutch and British Beaker males belonging to Y-haplogroup R1b-P312. This, of course, makes good sense, because both the Dutch and British Beakers are so called Rhenish Beakers.

The results are also in line with the observation that the Dutch Beakers are the quintessential Beakers in terms of physique, with three quarters or more sporting exceedingly brachycephalic, planoccipital skulls (like this).

Moreover, these two Beaker groups are among the most Yamnaya-like Beakers, with almost as much Yamnaya-related ancestry as the Corded Ware culture samples from Germany (~60% vs ~70%). As a result, in my PCA of ancient West Eurasian genetic variation the Dutch Beakers form a more or less continuous, west to east cline with these and other Corded Ware individuals that runs all the way to the Yamnaya cluster.


In the same PCA, the R1b-P312 Dutch and British Beaker males form a tight cluster at the apex of a Beaker cline that stretches to European Neolithic groups with no steppe ancestry. The only Beaker who is positioned clearly east of the Dutch/British R1b-P312 Beaker cluster is from Hungary, and in all likelihood he harbors recent Yamnaya ancestry because his Y-haplogroup is the Yamnaya-specific R1b-Z2103.


These findings potentially have important implications for the origins of the Dutch Beakers and the Beakers who dominated much of Central and Western Europe during the Late Neolithic and Bronze Age, and these are:

- the Dutch Beakers are unlikely to be the result of a recent migration from afar into what is now The Netherlands and surrounds, but rather the descendants, by and large, of the earlier local Single Grave (and thus Corded Ware) populations

- the R1b-P312 lineages in the Dutch and British Beakers probably derive from Single Grave R1b-P312, which suggests that R1b-P312 was common among some clans within the Corded Ware culture

- the spread of most of the Yamnaya-related or steppe ancestry and quintessential Beaker physique across the Beaker world and into Western Europe can probably be blamed on the massive expansions of Beakers from what is now The Netherlands and surrounds (ie. the Lower Rhine region)

- late Yamnaya groups contributed some ancestry to eastern Beaker groups, such as those in the Carpathian Basin, but the Dutch Beakers acquired their high level of Yamnaya-related ancestry from their Single Grave predecessors, who, in turn, acquired it from their proto-Corded Ware ancestors from the steppe.

Admittedly, I find the discussion about the origin of the Bell Beaker cultural package somewhat confusing. For all I know, it might have come from Iberia, the Carpathian Basin, or even North Africa. But this post isn't about that, it's about the homeland of the classic Beaker warrior male, with his R1b-P312, Corded Ware-like genome-wide genetic structure and brachycephalic skull. I'm almost certain now that this was the Lower Rhine region.

See also...

Hungarian Yamnaya > Bell Beakers?

Dutch Beakers: like no other Beakers

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

Friday, January 11, 2019

Hungarian Yamnaya > Bell Beakers?


Ever since the publication of the Olalde et al. Beaker paper (see here), there's been a lot of talk online about Hungarian Yamnaya as the most likely source of the Yamnaya-related, R1b-P312-rich northern Bell Beakers who went on to dominate much of Central and Western Europe during the Late Neolithic and Bronze Age.

Certainly, this is still possible, and we might find out soon if it's true because several Hungarian Yamnaya samples are apparently about to be published. But I wouldn't bet the proverbial farm on it just yet.

The most Yamnaya-like Beaker in the Olalde et al. dataset and ancient DNA record to date is from the Szigetszentmiklós burial site, which is indeed in present-day Hungary. But this individual, labeled I2787, is dated to just 2457–2201 calBCE, which isn't an early date for a Beaker and probably a couple hundred years past the proto-Beaker time frame.

Moreover, he belongs to Y-haplogroup R1b-Z2103, a paternal marker most closely associated in the ancient DNA record with eastern Yamnaya groups. And he doesn't exactly look like a classic northern Beaker, because he doesn't have a brachycephalic head with an exceedingly flat occiput (like this).

So I'd say that this is either an acculturated Beaker of recent Yamnaya origin, or perhaps the son of a Yamnaya father and Beaker mother. Below are several qpAdm mixture models that I ran to explore the latter possibility. They look very solid.

Beaker_Hungary_I2787
Beaker_Bavaria 0.442±0.045
Yamnaya_Samara 0.558±0.045

chisq 8.562
tail prob 0.73982
Full output

Beaker_Hungary_I2787
Beaker_Czech 0.441±0.045
Yamnaya_Samara 0.559±0.045

chisq 10.009
tail prob 0.61513
Full output

Beaker_Hungary_I2787
Beaker_The_Netherlands 0.576±0.062
Yamnaya_Samara 0.424±0.062

chisq 11.469
tail prob 0.489238
Full output

The idea that I2787 is a Beaker with recent Yamnaya ancestry isn't an original one. It was put forth very eloquently and convincingly months ago by the Bell Beaker Blogger himself:

Szigetszentmiklós Cemetery (Santa's Six Foot Elves)

I2786 is another Beaker male from the Szigetszentmiklós site who shows excess Yamnaya-related ancestry compared to most other Beakers. Again, it's likely that this individual harbors recent Yamnaya ancestry, because his Y-haplogroup is I2a-M223, which has been recorded in eastern Yamnaya alongside R1b-Z2103.

So my gut feeling for now is that Hungarian Yamnaya samples will mostly belong to Y-haplogroups R1b-Z2103 and I2a-M223, rather than R1b-P312, and thus they won't fit the bill in any obvious way as the population that may have given rise to northern Beakers.

One of the oldest individuals in the ancient DNA record belonging to R1b-P312 is I5748, a Beaker dated to 2579–2233 calBCE from the Oostwoud-Tuithoorn burial site in what is now West Frisia, The Netherlands.

Interestingly, this part of Northwestern Europe was home to the Single Grave population shortly before I5748 was alive. And the Single Grave culture is a variant of the Corded Ware culture. So can anyone tell me if there's any evidence that I5748 and his kind were relative newcomers to West Frisia, from, say, somewhere in the direction of the Carpathian Basin? If not, then what are the chances that northern Beakers are by and large the descendants of the Single Grave people?

In fact, there's not much difference in terms of genome-wide genetic structure between the Beakers from the Oostwoud-Tuithoorn site and Corded Ware people from what is now Germany. The Principal Component Analysis (PCA) below illustrates this well. But, you might say, Corded Ware males by and large belong to Y-haplogroup R1a-M417. Yep, but this doesn't mean that R1b-P312 wasn't common in some Single Grave clans.


At this stage, I don't have a clue where the northern Beakers might have come from, and unfortunately I don't have any inside information about the Y-haplogroups of Hungarian Yamnaya. I don't even know if any Single Grave samples are being analyzed. But I'll leave you with this map from a recent paper by French archeologist and Beaker expert Olivier Lemercier (see here). To me it suggests rather strongly that northern Beakers developed from the synthesis of Corded Ware newcomers to Western Europe and indigenous Western Europeans. As far as I can tell, that's what the paper basically argues as well.


See also...

Single Grave > Bell Beakers

Dutch Beakers: like no other Beakers

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