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Thursday, October 27, 2016

Strong mitogenomic continuity on the Armenian Plateau since the early Neolithic

Below is another abstract from the upcoming 6th DNA Polymorphisms in Human Populations conference in Paris. It was added to the abstract book after I first blogged about the conference here.

The authors are probably first testing mtDNA to check which of the samples have enough DNA for full genome sequencing or enrichment capture of genome-wide SNPs. So the fact that they managed to sequence so many mitogenomes means that we might soon see genome-wide data for most of the same samples.

The results make sense considering the genetic structure of present-day Armenians (see here). Indeed, I suspect that early Neolithic farmers from the southern Caucasus will come out looking very similar overall to present-day Armenians.

If so, this will probably be hailed by many as evidence supporting the Armenian Plateau Indo-European homeland theory. However, as I've already shown, it's very likely that the Armenian Plateau was affected by population movements from the Eastern European steppe during the Bronze Age which may have introduced Indo-European languages to the region (see here).

The origin of the Armenian people is heavily debated among historians and archaeologists. Despite a long history and vast archaeological records in Armenia, it has proven very challenging to infer the demographic events that led to the formation of Armenians as a distinct ethno-cultural group. To obtain a detailed understanding of the demographic events in Armenia across millennia, we study complete mitochondrial genomes from 49 ancient individuals covering 7800 years and compare them with that of modern Armenians (n=206) and seven neighboring populations (n=482). In this context, the lowest genetic distance was observed between the modern and ancient Armenians and this was also reflected in network analyses and discriminant analysis of principal components (dapc) showing genetic proximity between the ancient individuals and modern Armenians. We used Approximate Bayesian Computation (ABC) to test five different demographic scenarios of the Armenian population, and the simulations favored a model where both ancient and modern Armenians derive from the same source population. We conclude that there is a strong signal of continuity in the maternal Armenian gene pool during the last 7800 years.

Margaryan et al., 7800 years of Mitochondrial genetic continuity in Armenia, 6th DNA Polymorphisms in Human Populations, Talk Workhsop Genomic Demography, Musee de l’Homme, Paris, 7-10 December, 2016

Thursday, October 20, 2016

Sibero-Scythian idol's "racial realignment"

From The Siberian Times:

He has a massive nose with flared nostrils, wide open mouth, a bushy moustache and a beard. And yet all is not quite as it seems, for this sculpture, the most northerly of this genre in Asia, underwent an historic version of plastic surgery perhaps 1,500 years ago to give him a less Caucasian and more Asian appearance, according to experts.


So the original European look of the idol was changed to a more Asian countenance. Why would this happen?

'Judging by archeological finds found inside the grottos, this anthropomorphic idol was made during the Scythian time,' Yuri Grevtsov said. 'The first change came when the more European looking face was transformed to make it appear more Mongoloid was likely to have happened in the early Middle Ages with a shift of the population in the Angara River area,' he said.

In other words, incoming ethnic groups preferred the idol to be more akin to their own looks.

Source: Siberia's stone idols - 2,400 year old Ust-Taseyevsky idol 'underwent racial realignment early in Middle Ages', losing his European looks by Tamara Zubchuk

Tuesday, October 18, 2016

ASHG 2016 open thread

The relevant Twitter hashtag is #ashg. As far as I know Razib will be there. Some of the presenters might be sharing their posters online after their talks.

Arguably the most interesting part of the show, at least for us, is Iain Mathieson's poster presentation on Wednesday, October 19, on ancient DNA from early Balkan farmers. I made a prediction recently that we might see Y-haplogroup R1b in some of these samples, but don't be shocked if that turns out to be a dud.

Also, Iosif Lazaridis is doing a poster presentation on the 20th on the genomics of early farmers from the Near East. The talk will be based on his last paper that we've already discussed to death, but I suppose there's a chance he might reveal some new info.

Feel free to post your favorite tweets and links in the comments, but be as succinct as possible, so that people don't have to wade through too much drivel to find the good stuff. Thanks in advance for your cooperation.

See also...

ASHG 2016 abstracts

Friday, October 14, 2016

The peopling of South Asia: an illustrated guide

For your pleasure and my satisfaction: a nice little slide show on the ancient population history of South Asia. Click on the first image to get started. The images are based on my latest Principal Component Analysis (PCA) of the world (see here). Any other questions? Ask in the comments.

A fresh look at global genetic diversity

Below is my new Principal Component Analysis (PCA) or genetic map of global human population structure. I think it's a little bit special, and we can discuss why in the comments if anyone's interested. The datasheet is available here; it can be used to generate 2D and 3D PCA plots, and to model samples of your choice using the nMonte and 4mix R scripts.
Here are a few examples of nMonte mixture models for highly drifted populations that often confuse the crap out of standard population genetics programs.

Ulchi 64.45
AfontovaGora3 34.2
Dai 1.35


Ulchi 66.8
AfontovaGora3 33.2
Dai 0


Iran_Neolithic:I1945 38.6
Paniya 20.2
Yamnaya_Samara:I0357 17.4
Afanasievo:RISE509 16.55
Andronovo:RISE505 3.8
Iran_Late_Neolithic:I1671 3.45
Iran_Hotu:I1293 0


Paniya 54
Yamnaya_Samara:I0357 24.55
Iran_Neolithic:I1945 21.45
Afanasievo:RISE509 0
Andronovo:RISE505 0
Iran_Hotu:I1293 0
Iran_Late_Neolithic:I1671 0


Paniya 57.2
Iran_Neolithic:I1945 27.7
Yamnaya_Samara:I0357 15.1
Afanasievo:RISE509 0
Andronovo:RISE505 0
Iran_Hotu:I1293 0
Iran_Late_Neolithic:I1671 0


Paniya 24.9
Iran_Neolithic:I1945 23.15
Andronovo:RISE505 19.95
Iran_Late_Neolithic:I1671 17.85
Yamnaya_Samara:I0357 14.15
Afanasievo:RISE509 0
Iran_Hotu:I1293 0


It's interesting to note that the Dai from southern China help to improve the fit for Karitiana from the Amazon basin, but not the Wichi from Argentina.

Also, Andronovo significantly improves the fit for the East Iranian Pathans or Pashtuns, but clearly not as much for the Indo-Aryan Kalash, and none at all for Brahmins from India, who are also Indo-Aryans. Why? Don't know, but it might well be an important question in regards to the origins and spread of Indo-Iranian languages.

See also...

The peopling of South Asia: an illustrated guide

Wednesday, October 12, 2016

Across time in north-central Poland

Interesting new collection of ancient genomes here. The paper is coming very soon. Emphasis is mine.

The region of Kujawy in north-central Poland has a rich and thoroughly examined archaeological record of Neolithic and Early Bronze Age settlement. In that area, Neolithic transformation commenced with the arrival of farming communities of the Linear Pottery culture (LBK) in the second half of the 6th millennium BC. During the Early and Middle Neolithic, Kujawy was one of the northernmost and easternmost regions of central Europe with continuous early agricultural settlement associated with the Danubian Neolithic cultural tradition, bordering with the world of indigenous European Late Mesolithic and para-Neolithic hunter-gatherers. In the Middle Neolithic Kujawy was a major center of the eastern group of the Funnel Beaker culture. The third millennium BC brought to Kujawy, in succession, the Globular Amphora culture, Corded Ware culture, and, at the end of Neolithic period, the Bell Beaker Culture. Relics of all of those archaeological cultures, including inhumation graves, are often found at the same sites, offering a unique opportunity to track processes that shaped population development in central Europe. In this project, 17 ancient human genomes representing populations inhabiting a small area in Kujawy from the Middle Neolithic to the early Bronze Age were analyzed against other data for ancient and present-day Europeans. The main question is to what extent the frontier location of the studied region and its cultural and genetic ties along both north-south and east-west lines affected the population changes that shaped the genetic diversity of modern Europeans.

Polish Neolithic Genome Project. Study: PRJNA318237.

Monday, October 10, 2016

RIP with cannabis

Iron Age European-like people in what is now western China buried their dead with cannabis plants. Courtesy of

The skeleton has been identified as once belonging to a Caucasian man approximately 35 years old at the time of his death. Those that had buried him had placed a willow pillow under his head and had then placed a shroud of (13) cannabis plants over his chest reaching from below his pelvis at one end to the side of his face on the other. The skeleton lay in one of the 240 graves in the area known as the Jiayi cemetery. The people that lived in the area at the time were part of a Kingdom from 3,000 and 2,000 years ago known as the Subeixi. Prior research has shown the people lived there because it was an oasis in the desert, one that had become an important place for travelers to rest during their trek along the Silk Road.

Full article: Ancient skeleton covered in cannabis shroud unearthed in China

Based on this paper at Economic Botany:
Abstract: An extraordinary cache of ancient, well-preserved Cannabis plant remains was recently discovered in a tomb in the Jiayi cemetery of Turpan, NW China. Radiometric dating of this tomb and the archeobotanical remains it contained indicate that they are approximately 2800–2400 years old. Both morphological and anatomical features support the identification of the plant remains as Cannabis. Research discussed in this paper describes 13 nearly whole plants of Cannabis that appear to have been locally produced and purposefully arranged and used as a burial shroud which was placed upon a male corpse. This unique discovery provides new insight into the ritualistic use of Cannabis in prehistoric Central Eurasia. Furthermore, the fragmented infructescences of Cannabis discovered in other tombs of the Jiayi cemetery, together with similar Cannabis remains recovered from coeval tombs in the ancient Turpan cemetery along with those found in the Altai Mountains region, reveal that Cannabis was used by the local Central Eurasian people for ritual and/or medicinal purposes in the first millennium before the Christian era.

Hongen Jiang et al., Ancient Cannabis Burial Shroud in a Central Eurasian Cemetery, Economic Botany (2016). DOI: 10.1007/s12231-016-9351-1

Saturday, October 8, 2016

Dead cat bounce

Max Planck's Johannes Krause featured this curious map at a recent talk in Moscow on the Proto-Indo-European homeland debate (two hours into the clip here).

It appears to be an attempt to merge several of the main competing PIE homeland hypotheses into a single "hybrid model" under the umbrella of a modified version of the recently much maligned and now practically dead Neolithic Anatolian PIE hypothesis.

Make no mistake, it is an exceedingly strange effort that will be torn apart on several levels if it ever gets published.

Tuesday, October 4, 2016

Hurrians and the others

Here's another graph based on my new D-stats datasheet. The contrast in the population affinities of Armenia_MLBA (Middle Late Bronze Age) and Armenia_EBA (Early Bronze Age) is, at least for me, surprising.

Armenia_EBA or Kura-Araxes shows strong affinity to Caucasus populations, particularly those from the Northeast Caucasus. This is very cool, and it makes a lot of sense, because historical linguists and archaeologists generally consider Kura-Araxes people to have been early speakers of Hurrian, an ancient language thought to be closely related to present-day Northeast Caucasian languages.

But what's going on with Armenia_MLBA? I really didn't expect to see Latvians and Swedes sitting near the top of this graph. Clearly, someone from the north, closely related to present-day people from around the Baltic Sea, moved into the Armenian Plateau during or just before the Middle Bronze Age. But who were they?

I don't have a clue, but f4-stats suggest that they may have also been closely related to the Sintashta people of the Middle Bronze Age Ural steppes, who do appear very Northern European in terms of genome-wide genetic structure. The time frame fits, so does the expansive and militaristic nature of the Sintashta Culture (see here).

Yoruba Sintashta Armenia_EBA Armenia_MLBA f4 0.000676 Z 1.395
Yoruba Potapovka Armenia_EBA Armenia_MLBA f4 0.000459 Z 1.275
Yoruba Corded_Ware_CE Armenia_EBA Armenia_MLBA f4 0.000383 Z 0.933
Yoruba Poltavka Armenia_EBA Armenia_MLBA f4 0.000373 Z 0.814
Yoruba Andronovo Armenia_EBA Armenia_MLBA f4 0.000214 Z 0.486

By the way, these stats are based on transversion sites only to limit the effects of post-mortem damage on the ancient samples, some of which are not UDG treated.

Update 06/10/2016: As far as I can see, the qpAdm modeling software shows that Sintashta is indeed the best available proxy for the European-like admixture in Armenia_MLBA.


Armenia_EBA 0.799±0.069
Sintashta 0.201±0.069

chisq 7.181 tail prob 0.618257

Armenia_EBA 0.835±0.068
Andronovo (3) 0.165±0.068

chisq 9.549 tail prob 0.388179

Armenia_EBA 0.842±0.065
Andronovo (4) 0.158±0.065

chisq 9.742 tail prob 0.371809

Armenia_EBA 0.838±0.069
Srubnaya 0.162±0.069

chisq 9.993 tail prob 0.351059

Update 08/10/2016: By the way, the fact that Kura-Araxes shares high genetic drift with many Indo-European-speaking Southern Europeans, such as Albanians, has no bearing on its posited identity as an Hurrian-speaking population. That's because this inflated genetic affinity is mediated via ancient groups of largely Near Eastern origin not directly related to Kura-Araxes, such as Copper and Bronze Age pre-Indo-European Europeans. On the other hand, Caucasians, particularly Northeast Caucasians, in all likelihood do share direct ancestry with Kura-Araxes.

Monday, October 3, 2016

On Gamkrelidze-Ivanov's dubious map skills and then some

I've put together a new D-stats sheet that might be useful in the Indo-European homeland debate (see here). It features new samples from the EGDP dataset, with most of the stats based on over 750K SNPs. The stats are of the form D(Chimp,Ancient)(Mbuti,X).

The idea that Indo-Iranian languages arrived in Central and South Asia from the Armenian Plateau and/or eastern Anatolia during the Bronze Age, as per Gamkrelidze and Ivanov (check out their article here and, if you don't have access, crazy map here), is still popular with a lot of people. But it's most certainly a dud.

There's too much Bronze Age steppe ancestry in this part of the world, particularly among the more isolated Indo-Iranian populations like Pamir Tajiks and the Kalasha, as well as upper caste Indians, to ignore. At the same time, there is no hard data linking any of these groups to Bronze Age Armenia or Anatolia.

Also, some people in the comments here are still having problems comprehending the relationship between Eastern European Hunter-Gatherers (Eastern_HG or EHG) and Yamnaya, and how this relates to the issue of the Indo-European expansion from the Pontic-Caspian Steppe into other parts of Eastern Europe.

By and large the vast majority of EHG ancestry among present-day Europeans was mediated via Yamnaya or closely related groups from the steppe. How do I know? Because of the very close relationship between EHG and Yamnaya signals in present-day Europeans, and specifically Indo-European speaking Europeans, including those living in Eastern Europe.

Indeed, most of the EHG in Eastern Europe arrived there from the steppe as a package with Caucasus Hunter-Gatherer (Caucasus_HG or CHG) ancestry. Again, this is especially true for Indo-European speaking Northern and Eastern Europeans, who are generally hugging the line of best fit in these graphs for that reason. Note also that EHG and Yamnaya produce essentially the same results when plotted against CHG.

On the other hand, groups from far Northeastern Europe, where Uralic languages are currently spoken or were spoken until recently, appear to harbor inflated affinity to EHG and deflated affinity to CHG, putting them well above the line of best fit. These are also the same groups that show inflated East Eurasian, and more specifically Siberian, admixture, which is basically lacking in most Indo-Europeans. So I'm guessing that proto-Uralic speakers were mostly a mixture of EHG and East Eurasian, maybe with minor CHG.

Also worth noting is that Southern Europeans show inflated affinity to CHG and deflated affinity to EHG, putting them well below the line of best fit. This is because of their inflated Near Eastern ancestry (relative to Northern and Eastern Europeans) from the Neolithic and later periods, probably including CHG admixture that arrived in Southern Europe independently of EHG and Yamnaya/Yamnaya-related groups.

However, the ubiquitous presence of CHG across Europe today does not confirm Gamkrelidze and Ivanov's Armenian Plateau Indo-European homeland theory. That's because, unlike what their wacky map that I linked to above suggests, Eastern Europeans do not show any signs of ancestry from the South Caspian region (see here), which they clearly should if their Indo-European ancestors migrated en masse from Transcaucasia to the Pontic-Caspian steppe in an anti-clockwise direction around the Caspian Sea.

Rather, it appears that CHG gene flow diffused onto the Eastern European steppe with migrants coming directly from the Caucasus (see here). And, judging by the affinities of CHG and ancient groups in large part of CHG origin, these people were more likely the speakers of Caucasian languages than of Proto-Indo-European.

See also...

Hurrians and the others