Thursday, September 4, 2014
Ancient North Eurasian (ANE) admixture across Europe & Asia
Another update: ANE is the primary cause of west to east genetic differentiation within West Eurasia
This is an update of a supervised ADMIXTURE analysis that I ran earlier this year looking at ANE levels throughout Asia, the results of which I posted at my other blog (see here). Anyone wanna make a map?
here). That's not to say that the authors of this paper don't know what they're doing. Clearly they do, but at the fine-scale there's usually room for improvement no matter who you are.
For instance, in their paper in table S14.9 they list the Basques (in fact, French Basques) as 11.4% ANE, which sounds reasonable, although perhaps a little too high considering they admit that this population can be modeled as 0% ANE. On the other hand, they estimate the "North Spanish" to be 16.3% ANE.
Now, this reference set is actually from the 1000 Genomes project, where it's listed as Spaniards from Pais Vasco (ie. Basque Country). Essentially, what this means is that these are Basques from Spain. So why would Basques from France carry only 11.4% ANE, and Basques from Spain a whopping 16.3%? Not only that, but according to Lazaridis et al., these "North Spanish" also can be modeled as 0% ANE.
Obviously, something's not quite right there. Indeed, in my spreadsheet, the very same French Basques are listed as 7.4% ANE, while the Pais Vasco Spaniards as just over 8%. Call me crazy, and many do, but I think these results actually make good sense.
By the way, I made ten synthetic samples from the ANE allele frequencies from this test, and remarkably, in all of the analyses I've ran so far they behaved very much like MA-1 or Mal'ta boy, the main ANE proxy. Below, for example, is a Principal Component Analysis (PCA) of West Eurasia featuring these individuals. The result is very similar to that I obtained with Mal'ta boy (see here).
The synthetic ANE samples are available here. Feel free to play around with them, and if you do, please let me know what you discover.
As some regular visitors already know, I'm currently designing a new test for GEDmatch that will include various ancient components like ANE. Unfortunately, it might be a while before it's ready, simply because I want it to be as accurate as possible.
Eurogenes ANE K7
Corded Ware Culture linked to the spread of ANE across Europe