October 23, 2012

Ancient European DNA assessment with 'globe10'

I had previously assessed the same using globe4. See post on globe10 and associated spreadsheet.

The results appear similar to previous analyses overall, with the main features being the presence of "Southern" in Neolithic farmers (which peaks in the Near East), and its absence in hunter-gatherers. Some of the "Amerindian"-like admixture that was evident in globe4 has been "absorbed" by the Atlantic_Baltic (main European) component, but it is interesting that the Swedish hunter-gatherers (Ajv52/Ajv70) continue to show some Amerindian as well as other eastern (Australasian/South Asian) admixture that is lacking in the other samples. These individuals are outside the range of modern populations, but they overall tend to map to the most similar Atlantic_Baltic component with the addition of some eastern influences.

Also of interest is the fact the Oetzi is the only sample which shows a slice of West Asian (5.7%) admixture in this analysis. This was also the case in the previous one using K7b (1.4%). Gok4, on the other hand, the fellow Neolithic individual from Sweden seems to lack this. The arrangement of the Big Three West Eurasian components (Southern/West Asian/Atlantic_Baltic) has subtly changed in this calculator, but it would be tempting, nonetheless, to see in the little West Asian admixture that Oetzi has but Gok4 and the Mesolithic samples seem to lack, something of the vanguard of the arrival of the West Asian component in Europe. Obviously more samples are needed, including ones from the most interesting regions of the Balkans and Anatolia.


Davidski said...

That African influence shows up in the Brana sample in all analyses.

I wonder if there's any way to test/confirm whether it's real or the result of variation that no longer exists anywhere?

Anonymous said...

Either way Davidski it is still real, whether it persisted or not. I am satisfied because it is logical for Spain to have an Arrican component where other regions dont. I might have worried if it was only showing up in Sweden.

On the Amerindian thing. IMO the Amerind component most likely came from the West not the East. It is absent in central and East Asian samples. I think we need to be thinking about the mammoth hunters as occupying a circlet encompassing Asia and North America. Not a torc with a gap across the north Atlantic.

It might have been easier to cross at Beringia, but clearly there was still flow across the North Atlantic.

Anonymous said...

Some pictures on the two archaic Braña hunter gatherers: http://mariaxhe.blogspot.com/2012/06/el-csic-recupera-parte-del-genoma-de.html

According to a source they had long arms, short legs, smaller/heavier skulls, larger/broader jaws, and smaller hands.

Matt said...

@Davidski It seems kind of hard to test whether it is real (i.e. the product of admixture) until the adna samples are good enough quality to use with f statistics (they aren't at the moment, I guess, because otherwise that would be the first thing I'd expect Dienekes to do with them?).

I think maybe interesting would be to check whether these calculators based on contemporary populations recreate Fst differences for ancient populations.

I.e. look at the Fst we would expect that ancient populations to have based on the Fsts between components* and / or contemporary populations with similar component proportions and then compare this with actual Fsts between the ancient populations and other populations / components. If the numbers are a good fit, then the ancient populations can be thought of well described by the components, if not then they aren't.

But then I'd guess this would require a larger sample of adna.
*(e.g. a population with 50% component A and 50% component B should have the same Fst with C as (0.5FstAC + 0.5FstBC) [unless Fsts don't work that way?])

Garvan said...

The 3 (South-East Asian like) Behar et al PANIYA stands out as strange samples. I went back and re-read your blog on how you cleaned up this set (and followed the links to remind myself of the issues), so I wonder if you are sure they are PANIYA. They show 13.5% Australasian at K10, which does not even look like SEA.


Dienekes said...

so I wonder if you are sure they are PANIYA

They are unknown. They are labelled PANIYA because that's what they're labeled in the official data release. They're some kind of SE Asian data that is useful for ADMIXTURE fitting even if we don't know exactly what it is.