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Tuesday, November 20, 2018

Yamnaya: home-grown

I have some interesting news. It looks like Khvalynsk_Eneolithic I0434 can be used as essentially a perfect proxy for the Eneolithic steppe trio from Wang et al. 2018 when modeling the ancestry of the Yamnaya people of what is now the Samara region of Russia. Consider the qpAdm mixture models below, sorted by taildiff.

One of the best fitting models that also fairly closely matches archeological data, which suggest that Yamnaya was an amalgamation of the Khvalynsk, Repin and Sredny Stog cultures, is in bold. The worst fitting, and basically failed, models are listed below the dotted line. Note that almost all of these models feature reference populations from West and Central Asia.

Khvalynsk_I0434 + Iberia_ChL 0.681534184 > full output

Khvalynsk_I0434 + Globular_Amphora 0.525961242 > full output

Khvalynsk_I0434 + Iberia_Central_CA 0.515960444 > full output

Khvalynsk_I0434 + Sredny_Stog_I6561 0.485311962 > full output

Khvalynsk_I0434 + Varna 0.430411416 > full output

Khvalynsk_I0434 + Blatterhole_MN 0.328782809 > full output

Khvalynsk_I0434 + Baden_LCA 0.234307235 > full output

Khvalynsk_I0434 + Protoboleraz_LCA 0.231310724 > full output

Khvalynsk_I0434 + ALPc_MN 0.200002422 > full output

Khvalynsk_I0434 + Trypillia 0.193900977 > full output

Khvalynsk_I0434 + Balaton_Lasinja_CA 0.187031564 > full output

Khvalynsk_I0434 + Tiszapolgar_ECA 0.153940224 > full output

Khvalynsk_I0434 + Tisza_LN 0.145465993 > full output

Khvalynsk_I0434 + Balkans_ChL 0.111720163 > full output


Khvalynsk_I0434 + Armenia_EBA 0.0108890099 > full output

Khvalynsk_I0434 + Armenia_ChL 0.00882375703 > full output

Khvalynsk_I0434 + Levant_BA_North 0.0078751978 > full output

Khvalynsk_I0434 + Minoan_Lasithi 0.0675240088 > full output

Khvalynsk_I0434 + Peloponnese_N 0.046998906 > full output

Khvalynsk_I0434 + Hajji_Firuz_ChL 0.00269860335 > full output

Khvalynsk_I0434 + Shahr_I_Sokhta_BA1 0.00261908387 > full output

Khvalynsk_I0434 + Sarazm_Eneolithic 0.00120345503 > full output

Khvalynsk_I0434 + Seh_Gabi_ChL 0.00111898703 > full output

Khvalynsk_I0434 + Geoksiur_Eneolithic 0.000178295163 > full output

Khvalynsk_I0434 + Tepe_Hissar_ChL 0.000163698274 > full output

Khvalynsk_I0434 + Bustan_BA 0.000151088148 > full output

Why is this potentially important? Because unless Khvalynsk_Eneolithic I0434 was a recent migrant from the North Caucasus piedmont steppe, which is where the remains of the Eneolithic steppe trio were excavated, then Yamnaya's ethnogenesis might not have anything at all to do with Asia or even the Caucasus region. At least not within any reasonable time frame anyway. Here's a map showing the geographic locations of all of the populations relevant to the bolded mixture model above.

I won't be fussed if it turns out that the majority of the ancestry of the Yamnaya, Corded Ware and other closely related ancient peoples was sourced from the Eneolithic populations of the North Caucasus piedmont steppe. But I think it's useful to make the point that there are still very few ancient samples available from the steppes between the Black and Caspian seas, so we don't yet have much of a clue how the groups living throughout this region during the Eneolithic and earlier fit into the grand scheme of things.

See also...

Big deal of 2018: Yamnaya not related to Maykop

"The Homeland: In the footprints of the early Indo-Europeans" time map

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

Saturday, November 17, 2018

What happened to Maykop?

The Maykop culture was probably the result of migrations of settlers from Transcaucasia and beyond into the Northwest Caucasus during the Eneolithic and Early Bronze Age. Its peak lasted for roughly 700 years, from about 3700 BC to 3000 BC, after which it seems to have vanished suddenly. Why? Are there any decent papers on the topic?

The currently rather popular idea that Maykop gave rise to the Yamnaya culture is likely false. It was probably somehow involved in the rise of the contemporaneous Steppe Maykop culture in the steppes abutting the North Caucasus. But, thanks to ancient DNA, we now know that the people associated with this culture were distinct from those associated with Yamnaya.

In fact, when Steppe Maykop disappeared, Yamnaya spread into much of its former territory, and this turnover registers clearly in the time transect of ancient genomic data from the North Caucasus steppes (see here).

My view is that Maykop was generally an alien entity to the indigenous peoples of the steppes. These natives may have emulated it in some ways, but there's no need, I'd say, to go as far as to assume that Maykop was the vector for the spread of Indo-European languages into the Pontic-Caspian steppe.

Indeed, it seems to me that when the technological and economic advantages of Maykop over the steppe peoples eventually eroded, it couldn't hold its ground on the edge of a vastly different and perhaps largely hostile world, and quickly disappeared.

Here's a quote from a recent paper by Trifonov et al. on Maykop jewellery that I found very enlightening in regards to these issues (emphasis is mine):

These deep-rooted Near East traditions of ritualization of the production and use of jewellery pieces made of gold, silver and gemstones in the Maykop culture, on the one hand, maintained familiar canons of ritual behaviour and, on the other, made perception of sophisticated symbolism of gemstones more difficult for neighbouring cultures with different living standards, levels of social development and value systems to understand. The jewellery traditions of the Maykop culture had no successors in the Caucasus or the adjacent steppes. In the third millennium BC , the goldsmiths of Europe and Asia had to reinvent the technique of making thin-walled jointless gold beads from scratch (Born et al. 2009).

I do wonder, in fact, if the language spoken by the Maykop people was even part of a still existing language group, let alone if it belonged to the Indo-European language family.

See also...

Big deal of 2018: Yamnaya not related to Maykop

Sunday, November 11, 2018

The story of the earliest wine

Here's an interesting YouTube video about the origin and spread of wine making. Many of you might also appreciate the discussion about the Kura-Araxes Culture (about 26 minutes into the presentation)...

See also...

A potentially violent end to the Kura-Araxes Culture (Alizadeh et al. 2018)

How relevant is Arslantepe to the PIE homeland debate?

Likely Yamnaya incursion(s) into Northwestern Iran

Monday, November 5, 2018

On the spread of dairy pastoralism to East Asia (Jeong & Wilkin et al. 2018)

Over at PNAS at this LINK. Below is the abstract and a table with the uniparental haplogroups for the 20 ancient samples from the paper. Emphasis is mine.

Recent paleogenomic studies have shown that migrations of Western steppe herders (WSH) beginning in the Eneolithic (ca. 3300–2700 BCE) profoundly transformed the genes and cultures of Europe and central Asia. Compared with Europe, however, the eastern extent of this WSH expansion is not well defined. Here we present genomic and proteomic data from 22 directly dated Late Bronze Age burials putatively associated with early pastoralism in northern Mongolia (ca. 1380–975 BCE). Genome-wide analysis reveals that they are largely descended from a population represented by Early Bronze Age hunter-gatherers in the Baikal region, with only a limited contribution (∼7%) of WSH ancestry. At the same time, however, mass spectrometry analysis of dental calculus provides direct protein evidence of bovine, sheep, and goat milk consumption in seven of nine individuals. No individuals showed molecular evidence of lactase persistence, and only one individual exhibited evidence of >10% WSH ancestry, despite the presence of WSH populations in the nearby Altai-Sayan region for more than a millennium. Unlike the spread of Neolithic farming in Europe and the expansion of Bronze Age pastoralism on the Western steppe, our results indicate that ruminant dairy pastoralism was adopted on the Eastern steppe by local hunter-gatherers through a process of cultural transmission and minimal genetic exchange with outside groups.

Jeong & Wilkin et al., Bronze Age population dynamics and the rise of dairy pastoralism on the eastern Eurasian steppe, PNAS published ahead of print November 5, 2018

See also...

The mystery of the Sintashta people

Thursday, November 1, 2018

Big deal of 2018: Yamnaya not related to Maykop

I was going to write this post after the genotype data from the Wang et al. preprint on the genetic prehistory of the Greater Caucasus became available, because I wanted to demonstrate a few key points with analyses of my own. But I've got a hunch that the formal publication of the manuscript, and thus also the release of the data, has been indefinitely delayed for one reason or another. So here goes anyway, the big deal of 2018...

This year, ancient DNA has revealed that the populations associated with the Maykop and Yamnaya archeological cultures were genetically distinct from each other, and, in all likelihood, didn't mix to any significant degree. Case in point: an ADMIXTURE analysis from Wang et al. 2018.

No doubt, this is quite a shock for many people, especially those of you who consider Maykop to have been a Proto-Indo-European-speaking culture that either gave rise to Yamnaya or at least Indo-Europeanized it. So now, if you still want to see Maykop as the Indo-Europeanizing agent in the Pontic-Caspian steppe, you'll have to rely solely on archeological and linguistics data, and also keep in mind that ancient DNA has slapped you in the face.

In just a few years, ancient DNA has provided us with plenty of shocks, but this is arguably among the biggest.

However, I honestly can't say that it was a huge surprise for me, because I tentatively predicted this outcome more than two years ago based on a handful of mitochondrial (mtDNA) haplotypes (see here). Certainly, analyzing genome-wide genetic data is what I thrive on, but if that's off limits, then eyeballing even a few mtDNA markers can also be very useful.

Wang et al. easily demonstrate the lack of any meaningful genetic relationship between Maykop (including Steppe Maykop, which shows an unusual eastern influence) and Yamnaya using a range of methods. But, judging by their conclusion, in which they still seem to want to see Maykop as the said Indo-Europeanizing agent in the Pontic-Caspian steppe, they're not exactly enthused by their own results. And they also make the following claim (emphasis is mine):

Based on PCA and ADMIXTURE plots we observe two distinct genetic clusters: one cluster falls with previously published ancient individuals from the West Eurasian steppe (hence termed ‘Steppe’), and the second clusters with present-day southern Caucasian populations and ancient Bronze Age individuals from today’s Armenia (henceforth called ‘Caucasus’), while a few individuals take on intermediate positions between the two. The stark distinction seen in our temporal transect is also visible in the Y-chromosome haplogroup distribution, with R1/R1b1 and Q1a2 types in the Steppe and L, J, and G2 types in the Caucasus cluster (Fig. 3A, Supplementary Data 1). In contrast, the mitochondrial haplogroup distribution is more diverse and almost identical in both groups (Fig. 3B, Supplementary Data 1).

I'd say that what they're almost suggesting there is that the Caucasus and Steppe clusters, hence also the Maykop and Yamnaya populations, shared significant maternal ancestry. If this were true, then perhaps it might mean that the Pontic-Caspian steppe was Indo-Europeanized via female-biased migrations from Maykop? Yes, perhaps, if this were true. However, it's not.

To be sure, Yamnaya does show a close genome-wide genetic relationship with an earlier group from the North Caucasus region: the so called Eneolithic steppe people. But they can't be linked to Maykop or even the roughly contemporaneous nearby Eneolithic Caucasus population, and seem to have vanished, at least as a coherent genetic unit, just as Maykop got going. Wang et al. managed to sequence three Eneolithic steppe samples with the following mtDNA haplogroups: H2, I3a and T2a1b.

H2 is too broad a haplogroup to bother with, but here are the results for I3a and T2a1b from the recently launched AmtDB, the first database of ancient human mitochondrial genomes (see here).

In a database of 1,131 ancient samples, I3a shows up in just five individuals, all of them associated with Yamnaya-related archeological cultures and populations: Poltavka (BARu), Unetice (UNC), Corded Ware (CWC), and Bell Beaker (BBC). Similarly, T2a1b shows up in just four individuals, all of them associated with Corded Ware (CWC) and Bell Beaker-derived Bronze Age Britons (BABI). And if I go back a step to T2a1, then the list reveals two Yamnaya individuals from what is now Kalmykia, Russia.

Thus, using just two mtDNA haplotypes I'm able to corroborate the results from genome-wide genetic data showing a close relationship between Eneolithic steppe and Yamnaya. So like I said, useful stuff.

This obviously begs the question: what does the AmtDB reveal about Maykop mtDNA haplotypes, especially in the context of the genetic relationship, or rather lack of, between Yamnaya and Maykop? Yep, again, the AmtDB basically corroborates the results from genome-wide genetic data.

But don't take my word for it. Stick the currently available Maykop mtDNA haplogroups into the AmtDB and see what happens (for your convenience I've made a list available here). Considering the close geographic and temporal proximity of Maykop to Yamnaya, you won't see an overly high sharing rate with Yamnaya and closely related populations. Moreover, Maykop shows several haplogroups that appear highly unusual in the context of the Eneolithic and Bronze Age steppe mtDNA gene pool, and, instead, link its maternal ancestry to those of the early European farmers, West Asians or even Central Asians, such as HV, M52, U1b, U7b and X2f.

See also...

Yamnaya: home-grown

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

Big deal of 2016: the territory of present-day Iran cannot be the Indo-European homeland

Wednesday, October 24, 2018

Steppe Maykop: a buffer zone?

Unfortunately, the ancient data from the Wang et al. preprint still haven't been released online. As I've already pointed out many times, the manuscript conclusion looks horribly contrived (for instance, see here), but the data are awesome, and most of the preprint is quite solid.

One thing that I'd really like to do is to compare in detail each of the ancient populations from the preprint to groups of present-day and ancient speakers of Indo-European and Caucasian languages. What's the bet that, by and large, Eneolithic steppe will show strong links to Indo-Europeans, while Eneolithic Caucasus and Maykop to Caucasians?

But pending the release of the data, all I can do is look at what the authors have done with it.

Intriguingly, their analyses suggest that the Eneolithic steppe genotype may have vanished from the steppes abutting the Caucasus by at least 3500 BC. It seems to have been replaced there by a more heterogeneous gene pool, with both more easterly and southerly genetic affinities, associated with the Steppe Maykop archeological culture.

So who were the Steppe Maykop people and why did they show up, rather suddenly, in the North Caucasus steppes to seemingly clear out the Eneolithic steppe population from the region? I have a theory about that.

Both archeological and ancient DNA data show that the North Caucasus was being colonized by groups from Transcaucasia during the Eneolithic. But apparently this wasn't an entirely smooth and safe process, because these southern settlers were forced to build elaborate fortifications to keep the natives at bay. Indeed, at the site of Meshoko, in the Northwest Caucasus, there is evidence of such a fort being overrun and its community replaced, probably by a nearby indigenous group (see here).

On the other hand, during the Bronze Age Maykop period, the relations between the settlers from the south and the steppe peoples were apparently much more peaceful. So much so, in fact, that Maykop settlements weren't fortified. However, this was also the period when the North Caucasus steppes were home to the Steppe Maykop people.

So here's my theory: either by chance or design, Steppe Maykop territory was a buffer zone between Maykop and the potentially aggressive natives of the steppes to the north. I'm not necessarily suggesting that the Steppe Maykop people were foreign mercenaries hired by Maykop chiefs, but, in any case, they may have benefited economically in a variety of ways by keeping Maykop settlements safe.

Around 3000 BC, both Maykop and Steppe Maykop disappeared. The latter was replaced by the Yamnaya culture. I don't know much about this process. It may have been mostly driven by environmental impacts from climate change. But the fact that the Steppe Maykop population didn't contribute much, if any, ancestry to the Yamnaya people in the region suggests to me that it was a hostile takeover by Yamnaya.

Interestingly, the spread of Yamnaya into the North Caucasus steppes saw the return of the Eneolithic steppe genotype to the region, albeit in a modified form, with admixture from Middle Neolithic European farmers (see here).

See also...

A potentially violent end to the Kura-Araxes Culture (Alizadeh et al. 2018)

Monday, October 22, 2018

Y-haplogroup P1 in Pleistocene Siberia (Sikora et al. 2018 preprint)

Over at bioRxiv at this LINK. Below is the abstract, emphasis is mine. Two of the (unrelated) males from Yana RHS belong to Y-haplogroup P1 and mitochondrial haplogroup U2. Note that P1 is ancestral to Y-haplogroups Q and R.

Far northeastern Siberia has been occupied by humans for more than 40 thousand years. Yet, owing to a scarcity of early archaeological sites and human remains, its population history and relationship to ancient and modern populations across Eurasia and the Americas are poorly understood. Here, we report 34 ancient genome sequences, including two from fragmented milk teeth found at the ~31.6 thousand-year-old (kya) Yana RHS site, the earliest and northernmost Pleistocene human remains found. These genomes reveal complex patterns of past population admixture and replacement events throughout northeastern Siberia, with evidence for at least three large-scale human migrations into the region. The first inhabitants, a previously unknown population of "Ancient North Siberians" (ANS), represented by Yana RHS, diverged ~38 kya from Western Eurasians, soon after the latter split from East Asians. Between 20 and 11 kya, the ANS population was largely replaced by peoples with ancestry from East Asia, giving rise to ancestral Native Americans and "Ancient Paleosiberians" (AP), represented by a 9.8 kya skeleton from Kolyma River. AP are closely related to the Siberian ancestors of Native Americans, and ancestral to contemporary communities such as Koryaks and Itelmen. Paleoclimatic modelling shows evidence for a refuge during the last glacial maximum (LGM) in southeastern Beringia, suggesting Beringia as a possible location for the admixture forming both ancestral Native Americans and AP. Between 11 and 4 kya, AP were in turn largely replaced by another group of peoples with ancestry from East Asia, the "Neosiberians" from which many contemporary Siberians derive. We detect additional gene flow events in both directions across the Bering Strait during this time, influencing the genetic composition of Inuit, as well as Na Dene-speaking Northern Native Americans, whose Siberian-related ancestry components is closely related to AP. Our analyses reveal that the population history of northeastern Siberia was highly dynamic, starting in the Late Pleistocene and continuing well into the Late Holocene. The pattern observed in northeastern Siberia, with earlier, once widespread populations being replaced by distinct peoples, seems to have taken place across northern Eurasia, as far west as Scandinavia.

Sikora et al., The population history of northeastern Siberia since the Pleistocene, bioRxiv, posted October 22, 2018, doi:

See also...

Ust'-Ishim belongs to K-M526

Wednesday, October 17, 2018

A closer look at a couple of ancients from Hellenistic Anatolia

Not sure if anyone's mentioned or noticed this already, but the two currently available genomes from Hellenistic Anatolia (samples MA2197 and MA2198 from Damgaard et al. 2018) pack an impressive amount of steppe ancestry. Moreover, one of these individuals also shows obvious admixture from Central Asia.

This isn't particularly surprising, considering the well attested presence of Galatian Celts from deep in Europe and Cimmerians from the Eurasian steppe in Iron Age Anatolia. But it's worthy of note, because it's yet another example of ancient DNA correlating very strongly with archaeological data and historical records. Below are a couple qpAdm models for each of the two aforementioned Anatolians:

Anatolia_MLBA 0.429±0.073
Beaker_Hungary 0.571±0.073
chisq: 4.073
tail prob: 0.967727
Full output

Anatolia_MLBA 0.431±0.085
Hallstatt_Bylany 0.569±0.085
chisq: 4.056
tail prob: 0.968241
Full output


Anatolia_MLBA 0.469±0.037
Kangju 0.531±0.037
chisq: 12.091
tail prob: 0.356839
Full output

Anatolia_IA_MA2197 0.588±0.165
Cimmerian_Moldova 0.412±0.165
chisq: 11.657
tail prob: 0.390007
Full output

Hence, MA2197 can be modeled very successfully with more than 50% ancestry from a source closely related to the Bell Beakers from the Carpathian Basin and the presumably Celtic-speaking Hallstatt population of what is now Czechia. This almost certainly proves to me that MA2197 is largely of Galatian Celtic stock. The models for MA2198 aren't quite as statistically sound, but they still work, and indeed suggest that this individual might be in large part of Cimmerian origin.

See also...

Focus on Hittite Anatolia

Cimmerians, Scythians and Sarmatians came from...

Central Asian admixture in Hallstatt Celts

Monday, October 15, 2018

ASHG 2018 open thread

The American Society of Human Genetics (ASHG) annual meetings kicks off tomorrow in San Diego. Feel free to post anything near and far related to this event in the comment thread below.

You can explore this year's offerings via the online planner/abstract search located HERE. See anything really interesting? Here's what I found after a quick search using the term "ancient". Hopefully someone tweets from the South Asian talk.

Mount Lebanon provides an opportunity to study DNA from the ancient Near East

Reconstructing the peopling of old world south Asia: From modern to ancient genomes

Tracing the evolution of pigmentation-associated variants in Europe

Intriguingly, the Mount Lebanon abstract says this:

In addition, we found steppe-like ancestry in the Roman Period individuals which we have previously detected in present-day Lebanese but not in Bronze Age individuals. This supports our previous proposition that the steppe ancestry penetrated the region more than 2,000 years ago, and genetic continuity in Lebanon is substantial.

So what are we dealing with here exactly: admixture from the Hittites, Mittani, and/or Romans? Who does the Global25 point to?

See also...

The South Asian cline that no longer exists

Sunday, October 7, 2018

The resistance crumbles

Over the years some scientists from the Estonian Biocentre have been among the staunchest opponents of the idea that Bronze Age pastoralists originating in the steppes of Eastern Europe had a significant genetic and linguistic impact on South Asia (for instance, see here).

But this week they put out a review paper titled The genetic makings of South Asia [LINK] featuring the figure below. It's a nice visualization of the current state of understanding of the peopling of South Asia, and does acknowledge the major role that the said steppe pastoralists had in this process.

However, there's not a single mention of Y-haplogroup R1a in the review. This is surprising, considering the once common, but now no longer valid, claims that this paternal marker may have originated in India. I guess the grieving process will continue for a little longer for some.

My long-held opinion about the claims that R1a was native to India, Iran, Central Asia, or, indeed, anywhere but its actual homeland, which is certainly Eastern Europe, can be summarized as such: LOL!

See also...