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Thursday, November 29, 2018

The Uralic cline in the Global25


The Uralic cline is a concept that was discussed in some detail in the recent Lamnidis et al. palaeogenomics paper on the origin and spread of Siberian ancestry in Europe (see here). It pertains to the most northerly genetic cline that links the populations of West and East Eurasia, and is largely made up of Uralic-speaking peoples rich in Y-haplogroup N1c.

This is what the Uralic cline looks like when inferred from my Global25 Principal Component Analysis (PCA) data. Note that the plot features most of the Lamnidis et al. ancient samples, and they're all more or less sitting along my version of the said cline. The relevant datasheet is available here.

Admittedly though, as pointed out by Lamnidis et al., the Bolshoy samples probably aren't those of Uralic speakers because they're dated to 1523±87 calBCE, which predates most linguistic estimates of the spread of known Uralic languages into the Kola Peninsula. So the important question is why do they cluster along the Uralic cline and 2/2 of the male samples belong to N1c?

The most logical explanation, I'd say, is that the Uralic cline actually represents an older, pre-Uralic contact zone between the east and west. Nevertheless, I think it's likely that the Proto-Uralic language formed somewhere in this ancient contact zone, and the early Uralic-speaking peoples used it to their advantage to spread rapidly both east and west, especially during the Late Bronze/Early Iron Age, when they, and their N1c, finally reached the East Baltic region (see here).

See also...

Corded Ware people =/= Proto-Uralics (Tambets et al. 2018)

The mystery of the Sintashta people

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

Monday, November 26, 2018

Steppe ancestry in Chalcolithic Transcaucasia (aka Armenia_ChL explained)


In 2016 Lazaridis et al. published a paper featuring five ancient samples from the famous Areni-1 cave complex, in what is now Armenia, dated to the Chalcolithic (see here). This is how they described the ancestry of these ancients, which they labeled Armenia_ChL, in the supplementary PDF to their paper (page 94):

We do not have a pre-Chalcolithic sample from Armenia. We first model it [Armenia_ChL] as a 2-way mixture of any of WHG, EHG, CHG, Iran_N, Levant_N, Anatolia_N (Table S7.18), but we find no pair of these populations that could be ancestral to Armenia_ChL. We next model it as a 3-way mixture (Table S7.19), and determine that Armenia_ChL can be modeled as 18.3±1.5 EHG, 29.2±2.4% Iran_N, and 52.5±2.2% Anatolia_N. In the absence of a pre-Chalcolithic sample, we cannot be certain whether the Neolithic population of Armenia (which borders Anatolia from the east) was similar to that of Northwestern Anatolia and experienced gene flow from the east and north, or the reverse.

Since then, a lot of opinions have been posted in the comments at this blog and elsewhere about the possible origin and significance of Armenia_ChL. It seems to me that many people see Armenia_ChL as more or less an example of the indigenous Neolithic and Chalcolithic peoples of the South Caucasus. But some have argued that Armenia_ChL was in large part of Central Asian origin and concocted various mixture models to try and back up this rather strange claim.

To me, it was always obvious that Armenia_ChL harbored very recent admixture from the Pontic-Caspian steppe, because I couldn't reconcile its relatively high level of Eastern European Hunter-Gatherer (EHG) ancestry with a deep origin south of the Greater Caucasus range.

Moreover, in any decent Principal Component Analysis (PCA), like the one below, Armenia_ChL appears to form two subtle sub-clusters, with three of its individuals "pulling" more strongly towards Eastern Europe. This suggests that the EHG admixture in Armenia_ChL was present at variable levels and thus likely to be recent, because it didn't yet have time to diffuse evenly throughout the population.

Also, two out of the three Armenia_ChL individuals who are "pulling" north belong to steppe-specific mitochondrial (mtDNA) haplogroups. Armenia_ChL I1634 belongs to mtDNA haplogroup H2a1, which is seen in ancient samples from the Pontic-Caspian steppe associated with the Khvalynsk, Sredny Stog and Catacomb cultures, while Armenia_ChL I1409 belongs to mtDNA haplogroup U4a, which is found in numerous ancient samples, especially foragers, from the Pontic-Caspian steppe and other parts of Eastern Europe (see here). Coincidence? Surely not.


The idea that Armenia_ChL represents a long-standing indigenous Transcaucasian population also took a major hit recently with the release of the Wang et al. manuscript on the genetic prehistory of the Greater Caucasus. The preprint included samples from the Eneolithic Caucasus dated to earlier than Armenia_ChL (4594-4404 calBCE vs 4330-3985 calBCE) which looked typically Caucasian and lacked any discernible signals of ancestry from the steppe. Below is a PCA from Wang et al. featuring both the Eneolithic Caucasus and Armenia_ChL samples.


Unfortunately, modeling the recent ancestry of Armenia_ChL is still difficult, because the genotype data from Wang et al. haven't yet been released, so currently there is still no pre-Armenia_ChL sample available from the Caucasus for me to work with.

The earliest post-Armenia_ChL sample is Armenia_EBA I1658, dated to around a thousand years too late (3347-3092 calBCE). However, this individual is associated with the Kura-Araxes culture, which is generally seen as a direct successor to the native Neolithic cultures of Transcaucasia, and appears to be practically indistinguishable from the Eneolithic Caucasus trio in the Wang et al. PCA. Thus, pending the release of a pre-Armenia_ChL sample I might be able to use Armenia_EBA I1658 as an effective proxy for such a population.

Below are a couple of successful two-way qpAdm mixture models for Armenia_ChL and Armenia_ChL I1634, featuring Armenia_EBA I1658 and Sredny_Stog I6561 (the output for Armenia_ChL I1409 looked wobbly, probably due to a lack of markers). The reason I decided on Sredny_Stog from the North Pontic steppe as the surrogate for the steppe ancestry is because of the position of Armenia_ChL in the Wang et al. PCA relative to Eneolithc Caucasus, which suggests gene flow into the former from a more westerly steppe source than, say, Khvalynsk from the Samara region. Using these reference samples, the inferred ratio of steppe admixture in Armenia_ChL is around 15%, which I think makes sense, more or less, considering its position in both of the PCA above.

Armenia_ChL
Armenia_EBA_I1658 0.862±0.050
Sredny_Stog_I6561 0.138±0.050
chisq 17.038
tail prob 0.148174
Full output

Armenia_ChL_I1634
Armenia_EBA_I1658 0.836±0.065
Sredny_Stog_I6561 0.164±0.065
chisq 13.813
tail prob 0.312808
Full output

The presence of a significant, unambiguous signal of steppe ancestry in a group from a rich archeological site in Chalcolithic Transcaucasia might be very important in the context of the Proto-Indo-European (PIE) homeland debate. That's because it suggests that there was a movement of peoples potentially speaking dialects of PIE from the Eneolithic Pontic-Caspian steppe, the main candidate for the PIE homeland based on historical linguistics data, into cultural hubs south of the Caucasus, which may have acted as early dispersal points for Indo-European languages into other parts of the Near East, such as Anatolia. Admittedly, though, I'm still a fan of the Balkan route for the introduction of Hittite and other Anatolian languages into Anatolia, despite recent claims in scientific literature that this scenario wasn't corroborated by ancient DNA (see here).

Citation...

Lazaridis et al., Genomic insights into the origin of farming in the ancient Near East, Nature volume 536, pages 419–424 (25 August 2016), DOI: https://doi.org/10.1038/nature19310

See also...

Yamnaya: home-grown

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 highlighted 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.

Update 24/12/2018: I decided to repeat the analysis, but this time with Caucasus Hunter-Gatherers (CHG) as one of the outgroups (or right pops). The reason I initially didn't include CHG in the outgroups was because I didn't want to discriminate, perhaps unfairly, against West and Central Asians with high levels of CHG-related ancestry, and in favor of Europeans with no or minimal CHG-related input. But in my opinion, the new results clearly make more sense, with Sredny Stog and Varna at the top of the list.

Khvalynsk_I0434 + Sredny_Stog_I6561 0.410719649 > full output

Khvalynsk_I0434 + Varna 0.394089365 > full output

Khvalynsk_I0434 + Iberia_ChL 0.16554258 > full output

Khvalynsk_I0434 + Globular_Amphora 0.128348823 > full output

Khvalynsk_I0434 + Iberia_Central_CA 0.126100242 > full output

Khvalynsk_I0434 + Trypillia 0.135306664 > full output

Khvalynsk_I0434 + Baden_LCA 0.0853031796 > full output

Khvalynsk_I0434 + Protoboleraz_LCA 0.0766892008 > full output

Khvalynsk_I0434 + Tisza_LN 0.0661622403 > full output

Khvalynsk_I0434 + Tiszapolgar_ECA 0.0626469042 > full output

Khvalynsk_I0434 + Balaton_Lasinja_CA 0.0536293042 > full output

Khvalynsk_I0434 + ALPc_MN 0.0505788809 > full output

...

Khvalynsk_I0434 + Minoan_Lasithi 0.0439451605 > full output

Khvalynsk_I0434 + Balkans_ChL 0.0436885241 > full output

Khvalynsk_I0434 + Blatterhole_MN 0.0329758292 > full output

Khvalynsk_I0434 + Peloponnese_N 0.0181930605 > full output

Khvalynsk_I0434 + Armenia_EBA 0.014715999 > full output

Khvalynsk_I0434 + Armenia_ChL 0.0060437014 > full output

Khvalynsk_I0434 + Levant_BA_North 0.00514574731 > full output

Khvalynsk_I0434 + Shahr_I_Sokhta_BA1 0.00350059625 > full output

Khvalynsk_I0434 + Hajji_Firuz_ChL 0.00228771991 > full output

Khvalynsk_I0434 + Seh_Gabi_ChL 0.00117061206 > full output

Khvalynsk_I0434 + Sarazm_Eneolithic 0.001118931 > full output

Khvalynsk_I0434 + Bustan_BA 0.00021203609 > full output

Khvalynsk_I0434 + Tepe_Hissar_ChL 0.000200643323 > full output

Khvalynsk_I0434 + Geoksiur_Eneolithic 0.000175941977 > full output

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 https://doi.org/10.1073/pnas.1813608115

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