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Thursday, November 26, 2015

The Khvalynsk men

This is where the three Samara Eneolithic or Khvalynsk samples from the recent Mathieson et al. paper plot on my Principal Component Analysis (PCA) of ancient West Eurasia. They're labeled as Steppe_CA (steppe Copper Age). I've also marked them with their Y-chromosome haplogroups.

Individual 10433, belonging to Y-chromosome haplogroup R1a, is almost a pure Eastern hunter-gatherer, which is perhaps surprising, considering he was buried with copper artifacts. On the other hand, sample 10434, the one belonging to haplogroup Q1a, and positioned further east than the other two, appears to have been whacked over the head a few times and simply thrown into a ditch.

The PCA also has most of the other samples featured in Mathieson et al., including Neolithic Anatolians (labeled Anatolia_N), as well as extra samples from Allentoft et al. and Jones et al.

First Neolithic genomes from Greece

Just in at bioRxiv: Hofmanová et al., Early farmers from across Europe directly descended from Neolithic Aegeans

The main focus of the preprint are five Neolithic genomes from north-central Greece and northwestern Turkey. They're very similar to previously published Neolithic European and Anatolian samples, and strikingly different from present-day Greeks and Turks, pointing to major genetic turnovers in the Aegean region since the Neolithic.

The manuscript also reveals that, somewhat unexpectedly, two Mesolithic individuals from Thessaly, central Greece, belong to mtDNA haplogroup K1c. This is not a marker typical of other Mesolithic Europeans. It's a pity their genome-wide structure wasn't analyzed.

By the way, the key to Figure 2 lists Lithuanians and Mordovians as "Slavic", which is an oversight and needs to be corrected.

A bigger problem, however, is the mixture analysis presented in Figure 3. Loschbour-related ancestry is obviously inflated by East Asian admixture, hence it peaks among such groups as the Nogais of the North Caspian steppe, even though in reality they have very little Western European hunter-gatherer ancestry, if any.

Also, it seems to me that Ashkenazi Jews are used to represent Poles in the mixture analysis, because there's a slither of Yourba admixture in the pie-chart sitting over Poland. If so, that's a bit silly.

Tuesday, November 24, 2015

qpAdm tour of the Eneolithic/Bronze Age steppe

I didn't obsessively try to find the best fits. I just grabbed the reference samples that made the most sense based on previous analyses, archaeology and linguistics, and saved the best outcomes, which you can see below. A zip file with the full qpAdm output is available here.

Kotias 0.469
Karelia_HG 0.528
Han Chinese 0.003
chisq 3.534 tail prob 0.316424

Kotias 0.246
Karelia_HG 0.754
chisq 7.324 tail prob 0.119715

Kotias 0.489
Karelia_HG 0.511
chisq 1.749 tail prob 0.781875

Yamnaya_Samara 0.637
Esperstedt_MN 0.363
chisq 2.695 tail prob 0.610004

Kotias 0.478
Samara_HG 0.522
chisq 1.740 tail prob 0.783371

Kotias 0.473
Karelia_HG 0.527
chisq 2.133 tail prob 0.711255

Caucasus hunter-gatherer (CHG) Kotias provides very tight fits for all of these samples when coupled with Eastern hunter-gatherers (EHG) from Karelia or Samara, except for one of the Middle Bronze Age Poltavka individuals.

This outlier can't be modeled as a mixture of CHG and EHG, but is very nicely modeled as Samara Yamnaya and a Middle Neolithic (MN) sample all the way from Germany. What this suggests is that his CHG ancestry was mediated by Yamnaya, or a very similar population from the Early Bronze Age steppe, and that he has admixture from west of the steppe.

This correlates very well with archaeological data, which show intense contacts and the expansion of related archaeological cultures at this time across the forest steppe belt linking East Central Europe with the southern Urals. Actually, my hunch is that Poltavka outlier was an admixed migrant from the west returning to his ancestral homeland.

As we move deeper into the Middle Bronze Age, the exception becomes the rule. In other words, none of the samples can be modeled as simple mixtures of CHG and EHG.

Yamnaya_Samara 0.745
Anatolia_Neolithic 0.233
Han Chinese 0.023
chisq 4.311 tail prob 0.229778

Yamnaya_Samara 0.629
Esperstedt_MN 0.371
chisq 2.133 tail prob 0.711255

Yamnaya_Samara 0.589
Anatolia_Neolithic 0.411
chisq 3.936 tail prob 0.414759

Yamnaya_Samara 0.566
Starcevo_EN 0.434
chisq 3.939 tail prob 0.414306

Yamnaya_Samara 0.667
Baalberge_MN 0.333
chisq 4.447 tail prob 0.348858

Interestingly, Early to Middle Neolithic Anatolian and Hungarian farmers provide much better fits for Andronovo and Sintashta than Middle Neolithic farmers from Germany. Thus, a population closely resembling the Neolithic Anatolians may have lived somewhere near the Carpathians during the Bronze Age and contributed in a big way to the formation of Andronovo and Sintashta.

In this analysis I used ancient samples from the recently published Jones et al. and Mathieson et al. studies, available on request from the authors and at the Reich lab website here, respectively. The present-day samples are from the Human Origins dataset, also available at the Reich lab website.

See also...

Modeling Yamnaya with qpAdm

Thursday, November 19, 2015

First look at Caucasus hunter-gatherer Satsurblia

Many thanks to Jones et al. for providing us with a crucial piece in the puzzle that is the peopling of Europe. However, it has to be said that their Principal Component Analysis (PCA) is a bit of a mess. The reason it's a bit of a mess is because it suffers from projection bias or shrinkage.

In fact, the PCA actually contradicts their claim that Yamnaya was a mixture of Eastern European and Caucasus hunter-gatherers (EHG and CHG, respectively), because it fails to show that they form a cline (see here).

So what would happen if we ran a similar PCA that didn't suffer from projection bias? Well, I did just that, and in my PCA Yamnaya does look like a mixture of EHG and CHG (Satsurblia).

Jones et al. also argue that CHG is basically an offshoot of the so called Basal Eurasian clade (see Supplementary Fig. 2). However, to me, this makes no sense whatsoever.

I had a look at this issue with TreeMix, and my impression is that Satsurblia essentially represents a sister clade of Kostenki, albeit with Mota-related and MA1-related admixtures. It's hard to be more specific than that at this stage.

On the other hand, I certainly agree with Jones et al. when they say that CHG had a profound impact on the ancestry of present-day South and Central Asians. However, it's important to stress that this CHG influence probably arrived deep in Asia in at least two migration waves: one from the Caucasus or Near East and the other from Europe via the Eurasian steppe. It's easy to model this using qpAdm. Check out the zip file here.

Unetice_EBA 0.647
Satsurblia 0.213
Dai 0.140
chisq 0.379 tail prob 0.94446


Jones, E. R. et al. Upper palaeolithic genomes reveal deep roots of modern eurasians. Nat. Commun. 6:8912 doi: 10.1038/ncomms9912 (2015).

Update 21/11/2015: I now have the genotype data that was used in the paper. Below is a PCA with ancient genomes Bichon, Kotias and Satsurblia.

See also...

Caucasus hunter-gatherers (CHG) and the Indo-European question

Monday, November 16, 2015

Caucasus hunter-gatherers (CHG) and the Indo-European question

The recent Jones et al. palaeogenomics paper focusing on Caucasus hunter-gatherers (CHG) has this to say about the Indo-European and Indo-Aryan expansions:

CHG left their imprint on modern populations from the Caucasus and also central and south Asia possibly marking the arrival of Indo-Aryan languages.


It has been proposed that modern Indians are a mixture of two ancestral components, an Ancestral North Indian component related to modern West Eurasians and an Ancestral South Indian component related more distantly to the Onge [25]; here Kotias proves the majority best surrogate for the former [28,29] (Supplementary Table 10). It is estimated that this admixture in the ancestors of Indian populations occurred relatively recently, 1,900–4,200 years BP, and is possibly linked with migrations introducing Indo-European languages and Vedic religion to the region (28).


Finally, we found that CHG ancestry was also carried east to become a major contributor to the Ancestral North Indian component found in the Indian subcontinent. Exactly when the eastwards movement occurred is unknown, but it likely included migration around the same time as their contribution to the western European gene pool and may be linked with the spread of Indo-European languages. However, earlier movements associated with other developments such as that of cereal farming and herding are also plausible.

To their credit, in that last quote the authors leave open the possibility that CHG arrived in South Asia in multiple waves and with a variety of groups, including Neolithic farmers. Nevertheless, I'd say their comments are still confusing and perhaps also incredibly naive, because essentially they appear to be hoping that in CHG they've identified the Proto-Indo-European and Proto-Indo-Aryan genetic component.

Indeed, a lot of people actually believe that the overwhelming part of the West Eurasian admixture in South Asia should be attributed to the Indo-Aryans. But that's just stupid.

After all, many Dravidian groups that in all likelihood never spoke Indo-Aryan languages carry significant ratios of West Eurasian ancestry. Some of this influence can be explained by admixture with Indo-Aryans, but uniparental markers suggest that much of it was brought from West Asia by the Proto-Dravidians (see here).

Below is the aforementioned Supplementary Table 10. Note that two of the Indian populations that are best modeled with D-stats as mixtures of Kotias (one of the two CHG genomes) and Onge are Dravidian speakers (Mala and Vishwabrahmin or Viskwakarma, a Malayali community). Another three are Indo-Aryans (GujaratiC, GujaratiD and Lodhi), but with high levels of Ancestral South Indian (ASI) admixture, which suggests their ancestors might have been language shifters.

On the other hand, the three populations that are best modeled as Afanasievo (a pastoralist group from the Early Bronze Age steppe) and Onge are all Indo-Aryans (GujaratiA, GujaratiB and Tiwari).

But like I say, South Asia is a complex melting pot of Indo-Aryans, Dravidians, and several other linguistic groups, so a more comprehensive analysis than a comparison of a few D-stats is needed to unravel the origins of its people in a meaningful way.

By the way, Jones et al. also argue that CHG is basically an offshoot of the so called Basal Eurasian clade, which was first described in Lazaridis et al. 2014. I'm highly skeptical of this claim, and I might check it out after I get my hands on the CHG genomes.


Jones, E. R. et al. Upper palaeolithic genomes reveal deep roots of modern eurasians. Nat. Commun. 6:8912 doi: 10.1038/ncomms9912 (2015).

See also...

'Fourth strand' of European ancestry originated with (Caucasus) hunter-gatherers isolated by Ice Age

'Fourth strand' of European ancestry originated with (Caucasus) hunter-gatherers isolated by Ice Age

From a news feature about a forthcoming palaeogenomics paper:

"The question of where the Yamnaya come from has been something of a mystery up to now," said one of the lead senior authors Dr Andrea Manica, from Cambridge's Department of Zoology.

"We can now answer that as we've found that their genetic make-up is a mix of Eastern European hunter-gatherers and a population from this pocket of Caucasus hunter-gatherers who weathered much of the last Ice Age in apparent isolation. This Caucasus pocket is the fourth major strand of ancient European ancestry, one that we were unaware of until now," he said

Read more at: 'Fourth strand' of European ancestry originated with hunter-gatherers isolated by Ice Age

Update: the paper is now out and open access at Nature Communications.

The two ancient Georgian genomes belong to Y-chromosome haplogroup J. So it looks like I was right when I said that this type of ancestry mostly entered the European steppe from the Caucasus via female mediated gene flow during the Bronze Age (see here and here).

However, one of the Eastern European Hunter-Gatherers (EHG) from Mathieson et al. 2015 also belonged to haplogroup J. This suggests that there was intermittent gene flow, including some paternal gene flow, between the Caucasus and the steppe well before the Bronze Age.

Nevertheless, it's now even more difficult to accept that Y-haplogroup R1 and the Proto-Indo-Europeans might have originated south of the steppe. Clearly, R1 appears to be a steppe marker from way back, and I seriously doubt that Indo-European languages were introduced into highly patriarchal steppe societies by female migrants from the Caucasus.

Image credit: Nature Communications,

The Aryan Trail (3500 - 1500 BC)

Cool little website here titled The Aryan Trail (3500 - 1500 BC). A lot of the stuff will look very familiar to those who've been following this blog and the latest ancient DNA results, which, among other things, include the discovery of Y-chromosome haplogroup R1a-Z94 in a sample from a Kurgan burial at Potapovka, near the Volga River, Russia, dated to 2925-2536 cal BCE (see Poltavka_outlier, ID I0432, Mathieson et al. 2015). Of course, R1a-Z94 is one of the most common Y-chromosome haplogroups amongst present-day Indo-Aryans.

Excavations conducted from 1985-1988 in Potapovka exposed four burial mounds, or kurgans, dated between 2200-2000 BC. Beneath kurgan 3 the central grave pit had remains of a man buried with at least two horse heads and the head of a sheep, in addition to pottery vessels and weapons. After the grave pit was filled, a human male was decapitated, his head was replaced with the head of a horse, and he was laid down over the filled grave shaft. This unique ritual provides a convincing antecedent for the Rig Vedic myth of Dadhyac Atharvan who knows the secret of making Soma juice, the nectar of immortality. The Asvins insists that Dadhyac tell them the secret. He refuses. They cut off his head and replaces it with the head of a horse, through which he becomes an oracle and tells them the secret.

Source: The Aryan Trail (3500 - 1500 BC)