Tuesday, June 30, 2015

Population genomics of Bronze Age Eurasia, Allentoft et al. 2015

We have yet more ancient DNA, this time we have 101 low coverage (low number of SNPs to work with) ancient genomes from across various parts of Eurasia strewn across the map below:


We have ancient genomes from Bronze Age Armenia, the Sintasha culture, more Yamnaya genomes, results from Andronovo & Afanasievo cultures and so much more. It's all really intriguing and to a great extent like Haak et al. 2015; centers around mapping and supporting the expansion of the Indo-European languages, with the Pontic-Caspian Steppe origin hypothesis for the language family  being backed up by genetic data yet again.


Rough spread of the Indo-European languages in their homelands

"The Bronze Age of Eurasia (around 3000–1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought."

It seems to back-up the slightly older Haak et al.'s data, this time with newer Yamnaya & Corded Ware Culture samples and proves once again that there was a massive westward migration from the Pontic-Caspian Steppe into the rest of Europe where subsequent mixing occurred between the pastoral nomadic peoples from the steppe and Early European Farmers of which modern Sardinians are the best preserved example of as a genetic isolate group in Europe that did not incur much steppe-related ancestry at all.



There seems to also be (as you can see above) a sort of resurgence of Western European Hunter-Gatherer (WHG) ancestry across Europe as most Europeans can now be modeled as a three-way mixture between Early European Farmers, Western European Hunter-Gatherers & the Yamnaya. So Haak et al. (granted, I didn't doubt their data at all) was on the money and is now backed up by another study with newer samples altogether. 



The steppe expansion into the rest of Europe is represented most strongly by the peoples of the Corded Ware culture who genomically just look like a later westward extension of the Yamnaya; looking almost identical to them on a genetic level. This new study (Allentoft et al.) backs this fact we were already aware of up via Haak et al. up as well but adds even more interesting data thanks to the sheer geographic scope of its sampling. 



It for example finds that the peoples of the Sintashta culture seem very genetically similar to Corded Ware peoples:

"Although we cannot formally test whether the Sintashta derives directly from an eastward migration of Corded Ware peoples or if they share common ancestry with an earlier steppe population, the presence of European Neolithic farmer ancestry in both the Corded Ware and the Sintashta, combined with the absence of Neolithic farmer ancestry in the earlier Yamnaya, would suggest the former being more probable."

The former seems probable to me as well, especially in that they carry Early European Farmer ancestry (referred to as "Neolithic Farmer" in this case) so it's quite likely that what the Sintashta culture's people are is an eastward migration from peninsular Europe back into the steppe belt of Eurasia. 




This study truthfully has a lot to talk about and as the first few lines of this blog post say; has 101 ancient genomes to share so there's a lot to touch upon that I may not dive into within this post but with consequent posts, however; for the time being I'd touch upon a few more interesting things they shared such as what seems to be evidence of an eastward migration from the Pontic-Caspian Steppe itself:



"The Early Bronze Age Afanasievo culture in the Altai-Sayan region is genetically indistinguishable from Yamnaya, confirming an eastward expansion across the steppe, in addition to the westward expansion into Europe. Thus, the Yamnaya migrations resulted in gene flow across vast distances, essentially connecting Altai in Siberia with Scandinavia in the Early Bronze Age."
So there was both a westward expansion (The Corded Ware Culture) from the Steppe into peninsular Europe which profusely shaped modern European demographics as I mentioned above and also an early (~3000 BCE) expansion from the steppe by peoples genetically identical to the Yamnaya who made their way into South Siberia. (The Afanasievo Culture). 

Some other information I found quite intriguing would be that the later Central Asian Andronovo culture's people seemed to have been very genetically similar to the peoples of the Sintashta culture whilst being clearly distinct from the Yamnaya and Afanasievo. The study ascertains that they represent a "temporal and geographic extension of the Sintashta gene pool". 

What's even more intriguing though is that they seem to prove that by the late Bronze Age to Iron Age; the Andronovo were essentially replaced by more "multi-ethnic" cultures owed to eventual intermixing with "East Asian" peoples.

"Towards the end of the Bronze Age in Asia, Andronovo was replaced by the Karasuk, Mezhovskaya, and Iron Age cultures which appear multi-ethnic and show gradual admixture with East Asians, corresponding with anthropological and biological research." 



 This seems to back up the kind of data one would get if they utilized the Eurogenes K=8 model and ran contemporary Central Asians (Kazakhs et al.) through it: Central Asians prove to be a genetic mixture between West & East Eurasians; in this case Bronze Age peoples from Europe and East Asians.

However the study seems to find that Iron Age Central Asians prove more West Eurasian than contemporary Central Asians so there seems to have been an increase in East Asian ancestry since the Iron age...

On an extra note; it's not simply the Corded Ware who clearly show input from the Yamnaya during the Bronze Age but various other cultures across Europe at the time who show what looks to be a "Caucasian" component as the study notes; however this Caucasian component isn't owed to ancestry from the Southern Caucasus but from the Steppe:

"Although European Late Neolithic and Bronze Age cultures such as Corded Ware, Bell Beakers, Unetice, and the Scandinavian cultures are genetically very similar to each other, they still display a cline of genetic affinity with Yamnaya, with highest levels in Corded Ware, lowest in Hungary, and central European Bell Beakers being intermediate. Using D-statistics, we find that Corded Ware and Yamnaya individuals form a clade to the exclusion of Bronze Age Armenians showing that the genetic ‘Caucasus component’ present in Bronze Age Europe has a steppe origin rather than a southern Caucasus origin. Earlier studies have shown that southern Europeans received substantial gene flow from Neolithic farmers during the Neolithic."

 The chief thing I noticed in this case is that they note this "Caucasian component" but this study simply doesn't go into some rather intriguing subjects the Haak et al. study did which would be what seems to have "formed" the Yamnaya themselves. Haak et al. touches upon two populations it called "Eastern European Hunter-Gatherers" (which it seemed to imply (if I recall correctly) were "Ancient North Eurasian (ANE) MA-1 related ancestry" + Western European Hunter-Gatherer") & what they dubbed an "Armenian-like" / "Caucasian-like" population.

 It further seemed to say that these two populations (Eastern Hunter-Gatherers and the Caucasian-like population)  intermixing is what ultimately created the Yamnaya. Making the Yamnaya the mixture between ANE, ENF & WHG that they seem to be:

 The study doesn't go into this at all... It doesn't really even touch upon Eastern European Hunter-Gatherers or back up the idea that they seem to look like a mixture between ANE & WHG like the Karelian Hunter-Gatherer from Haak et al. did even via the Eurogenes K=8 model:


We don't even know if this model is correct. Is EHG a mixture between "ANE" & "WHG" or something else entirely that just shares ancestry with MA-1/ "Ancient North Eurasians"... As David (the author of Eurogenes) tells me; you could even model WHG as "EHG + something as of yet not sampled" so despite what I thought in my former post; there's still honestly some research to be done into "Eastern European Hunter-Gatherers".

 There's nothing in Allentoft et al. about this Caucasian-like population that Haak et al. seemed to imply brought West Asian & Basal Eurasian carrying ancestry into the Yamnaya ("ENF") either. It would've been rather riveting if they went into all that but alas... They didn't.

Ultimately though, one thing I would keep in mind at this point is that the old "Europeans = ANE + WHG + EEF" model from Lazaridis et al. 2013-14 is clearly no longer the case. Instead; most Europeans are basically a mixture between Yamnaya descended Pontic-Caspian Steppe pastoralists (who themselves carry ANE ancestry/ share ancestry with MA-1), WHGs & EEFs.

 Though of course; the Yamnaya themselves are not purely ANE but a mix between ANE/ MA-1 related ancestry, WHG & "ENF" (The EEF component with its WHG removed).

 At any rate; there's obviously a lot more to say about this amazing and extensive new paper but I figured I'd stop here for now. Frankly, this is a bit of a messy post in my humble opinion especially because this study has quite a bit of for one to touch upon and I suppose I tried to ram in several different things into this one post.

 The best advice I can offer for now to anyone looking to learn more about these samples would be to keep up with the Eurogenes blog where the author has some interesting things to share. Alongside that; make sure to actually read the full study as well as its supplemental.

Reference List:



Notes:

1. Don't take the "East Eurasian" in the Karelian Hunter-Gatherer seriously, it's probably not real (granted, it could be as we lack confirmation of it via formal stats) in my humble opinion. Don't make much of anything in either the Yamnaya or Karelian Hunter-Gatherer that isn't ANE, WHG or ENF seriously at all, to be quite frank.

 2. Some highly interesting notes from a linguist friend of mine: [-]

 3. Now, there's a lot of interesting new ancient Haplogroup data available via this study (some notes from my linguist compatriot & an image from the Allentoft et al. itself just to share a few) and while I myself am not known to touch upon Haplogroups much (my knowledge of them is not as keen as my knowledge of autosomal DNA); I highly recommend looking into this study if you're interested in Haplogroups.
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