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Friday, June 26, 2015

Genetic substructures among Late Neolithic/Bronze Age Scandinavians


I may have discovered an interesting pattern in the Allentoft et al. data. It seems that during the Late Neolithic/Bronze Age, Scandinavia was populated by two somewhat different populations; one characterized by Y-Chromosome haplogroup R1b and a genome-wide genetic structure typical of present-day Northwestern Europeans, and another by Y-Chromosome haplogroup R1a and a relatively more eastern genome-wide genetic profile.

Below are two Principal Component Analyses (PCA), both featuring ancient Swedish genomes classified as part of the Late Neolithic Battle-Axe archeological culture. However, the first sample clusters near present-day Norwegians and belongs to Y-haplogroup R1b-U106, which is nowadays typically known as a Germanic paternal marker. On the other hand, the second sample clusters among present-day Russians and Mordovians, from all the way near the Volga, and belongs to Y-haplogroup R1a-Z645, which very likely expanded from Eastern Europe during the Late Neolithic.




Here's another example of basically the same thing, but this time with two ancient genomes from Denmark. If you're having trouble finding the ancient samples, download the PDF files and type their IDs in the PDF search field.



Coincidence? Probably not, but we obviously need more samples to confirm these results and establish that there is indeed a pattern.

Citation...

Allentoft et al., Bronze Age population dynamics, selection, and the formation of Eurasian genetic structure, Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

Monday, June 22, 2015

First look at an ancient genome from Neolithic Anatolia


Felix at GGT is in the process of uploading the genomes from the recent Pinhasi et al. paper. The file for the early Neolithic sample from Barcin, Turkey, is basically ready. I analyzed it with my K8 model and got these results (click on the image to enlarge).


I was only able to use a couple hundred SNPs for the test, so the outcome can't be taken too seriously. But it does make sense. The lack of Ancient North Eurasian (ANE) ancestry isn't surprising, because it mirrors the results of early European farmers we've seen to date.

Moreover, the relatively high level of Western European Hunter-Gatherer (WHG) ancestry, or at least something very similar, is also in line with expectations, considering that the sample was dug up in far western Anatolia, almost on the European border.

I also ran an Identical-by-State (IBS) affinity test using the Human Origins dataset and around 1800 SNPs. The results broadly back up the K8 analysis, with southern Europeans topping the list.


Citation...

Pinhasi R, Fernandes D, Sirak K, Novak M, Connell S, Alpaslan-Roodenberg S, et al. (2015) Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone. PLoS ONE 10(6): e0129102. doi:10.1371/journal.pone.0129102

See also...

The Near East ain't what it used to be

Thursday, June 18, 2015

Paul Heggarty: desperate or clueless?


Over at Diversity Linguistics Comment, Paul Heggarty of the Max Planck Institute for Evolutionary Anthropology (Leipzig) puts his foot in his mouth with a long-winded and rather whiny comment piece about two recent ancient genomics papers, Haak et al. and Allentoft et al., and the PIE question.

I don't have the time or energy right now to pick apart in detail Heggarty's ramblings, so I'll only focus on a couple of points. Firstly, here's a modified figure from Haak et al. that Heggarty put up with his post, and below that a couple of quotes with his explanation.

These data imply that Uralic-speakers too would have been part of the Yamnaya > Corded Ware movement, which was thus not exclusively Indo-European in any case. And as well as the genetics, the geography, chronology and language contact evidence also all fit with a Yamnaya > Corded Ware movement including Uralic as well as Balto-Slavic.

Both papers fail to address properly the question of the Uralic languages. And this despite — or because? — the only Uralic speakers they report rank so high among modern populations with Yamnaya ancestry. Their linguistic ancestors also have a good claim to have been involved in the Corded Ware and Yamnaya cultures, and of course the other members of the Uralic family are scattered across European Russia up to the Urals.

These are exceedingly naive and stupid comments from someone representing the Max Planck Institute. Perhaps as an ardent supporter of the Anatolian hypothesis he's feeling more than a little desperate at this point and clutching at straws? That's because anyone with even a basic grasp of European linguistics and genetics should know that:

- present-day Hungarians and Estonians speak Uralic languages, but they are of course overwhelmingly of Indo-European origin, which is easily seen in their genome-wide and uniparental DNA

- other Uralic speakers, further to the north and east, in the forest zone away from Indo-European influence, are clearly distinct from the vast majority of Indo-European speaking Europeans, because they show significant levels of recent Siberian ancestry, which was missing among the Yamnaya and Corded Ware people, and appears to be an Uralic-specific genetic signature

- therefore, it's highly unlikely that Uralic-speakers were also part of the Yamnaya > Corded Ware movement; rather, early Uralics in all likelihood began to move west across the forest zone well after the Yamnaya and related expansions from the steppe.

Heggarty also can't get over the fact that not all Indo-European speaking Europeans harbor as much Yamnaya-related ancestry as Northern and Eastern Europeans.

Above all, the Yamnaya > Corded Ware impact is much less widespread in Europe than Indo-European languages are. Much of southern Europe has spoken Indo-European languages from our earliest records (Latin and its ‘Italic’ relatives, Greek, Albanian and various other Indo-European languages of the Balkans, now extinct).

Some (low) proportions of apparent ‘Yamnaya’, ‘Corded Ware’ and north European ancestry do appear in present-day populations of southern Europe (Haak et al. 2015 Figure 3b). But such north to south population admixture is in any case expected from the historical period. The collapse of the Roman Empire and the migrations of the early medieval period were defined by major invasions and settlements of Slavic and Germanic-speaking populations into southern Europe.

The levels of Yamnaya-related admixture among present-day Southern Europeans are significant and plenty enough to explain why most of them speak Indo-European languages. All of this Yamnaya-related admixture cannot be explained by Germanic and Slavic incursions into Southern Europe during the early medieval period, because:

- most Southern European populations show very little admixture from Northern and Eastern Europe dating to this time frame (see Ralph and Coop 2013)

- R1b-M269 is the most common Y-chromosome haplogroup across much of Southern Europe, and its subclade structure among Southern Europeans, as well as the ancient DNA data from Haak et al. and Allentoft et al., suggest that the vast majority of it arrived there from somewhere in the east before the historical period but after the Neolithic.

About the only worthwhile point that Heggarty makes is that we need more ancient DNA, especially from more southerly regions, to help solve the PIE riddle once and for all.

He probably thinks that the new data will back up the Anatolian hypothesis. It won't. If Heggarty could actually understand the data from Haak et al. and Allentoft et al., he'd already know that the jig was up for his pet theory.

See also...

The ancient DNA case against the Anatolian hypothesis

Population genomics of Early Bronze Age Europe in three simple graphs

Ancient genomes from NE Europe suggest the tandem spread of Siberian admixture and Uralic languages into the region >3,500 ya

Wednesday, June 10, 2015

101 ancient Eurasian genomes (Allentoft et al. 2015)


It'll take me a while to digest all of the information in this massive new Allentoft et al. paper. But I've already noticed that, just like in Haak et al. 2015, the Yamnaya samples are again from the eastern half of the Yamnaya horizon. This time, however, not all of the Yamnaya individuals carry Y-haplogroup R1b; one of the five samples belongs to Y-haplogroup I2a (see here).

So I'm wondering what more westerly Yamnaya sites will reveal in the future, considering the predominance of Y-haplogroup R1a among the Corded Ware individuals sampled to date, and the close genome-wide relationship between the Yamnaya and Corded Ware?

Abstract: 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.

Allentoft et al., Population genomics of Bronze Age Eurasia, Nature 522, 167–172 (11 June 2015) doi:10.1038/nature14507

See also...

R1a-M417 from Eneolithic Ukraine!!!11