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Sunday, July 26, 2015

Global PCA of selected Late Neolithic/Bronze Age Eurasians


I was curious how the Bronze Age steppe and Corded Ware genomes from the Rise dataset would behave in Principal Component Analyses (PCA) alongside populations from across the globe. Ten genomes had enough high confidence (transversion) markers to be analyzed accurately in such a way. I also ran an Iron Age Swedish sample, just to see how it differed from the older genomes.

Click on the links to go to my drive to download the plots. If you're having trouble finding the ancient samples, type their IDs into the PDF search field and hit enter.

RISE509_Afanasievo
RISE509_Afanasievo
RISE509_Afanasievo

RISE511_Afanasievo
RISE511_Afanasievo
RISE511_Afanasievo

RISE500_Andronovo
RISE500_Andronovo
RISE500_Andronovo

RISE505_Andronovo
RISE505_Andronovo
RISE505_Andronovo

RISE00_Corded_Ware
RISE00_Corded_Ware
RISE00_Corded_Ware

RISE94_Corded_Ware
RISE94_Corded_Ware
RISE94_Corded_Ware

RISE493_Karasuk
RISE493_Karasuk
RISE493_Karasuk

RISE496_Karasuk
RISE496_Karasuk
RISE496_Karasuk

RISE548_Yamnaya
RISE548_Yamnaya
RISE548_Yamnaya

RISE552_Yamnaya
RISE552_Yamnaya
RISE552_Yamnaya

RISE174_Iron_Age_Scandinavia
RISE174_Iron_Age_Scandinavia
RISE174_Iron_Age_Scandinavia

I can't see any major surprises. But I do find it remarkable how very European the Andronovo individuals appear on these plots. Keep in mind that they're ~3,000-year-old samples from the Altai region of Russia. Their ancestors probably emigrated there from the Trans-Urals steppe sometime during the Middle Bronze Age.

The Andronovo Culture was succeeded in the Altai region during the Late Bronze Age by the Karasuk Culture, which was probably a new composite of local and perhaps foreign groups. Interestingly, the Karasuk samples featured above are obviously of mixed European/East Asian origin.

Note also that the Afanasievo and Yammnaya individuals fall outside the range of present-day European variation in many of the dimensions, basically as if they were pulling towards the Karitiana Indians of the Amazon. No doubt, this is their excess ANE talking.

By the way, I recently ran some of the same samples in PCA limited to West Eurasian populations. You can see the results here.

6 comments:

Mike Thomas said...

How much ANE do Karitania have ?

Davidski said...

Around 42%.

Grey said...

curiouser and curiouser

Matt said...

EEF vs ENA defines the second dimension so you and many samples are not that close to EEF. I wonder if a lot of EEF samples together would create a cluster even further out from Sardinian, or not.

Andronovo in these world terms (defined in many ways by similarity to Asian and African outgroups) is about as close to Lezgin, Chechen, Adygei as it is to Estonian, while they are more distinct with a WE view.

Similarly in these terms, Corded Ware is overlapping North/East Europe (Scotland, Norway, Lithuania) close by Georgia, Armenia.

Davidski said...

I'd need several high coverage EEF samples to do this, but Stuttgart almost sticks out beyond the Sardinians by itself.

https://drive.google.com/file/d/0B9o3EYTdM8lQOTQxX2ZRWFJnQUE/view?usp=sharing

At the same time though, in dimension 1 it's closer to Sub-Saharan Africans than most Europeans are.

andrew said...

It is very hard to distinguish the targets from the other points on the plots visually.