MAJOR recalibration of Near Eastern DNA in Geno 2.0+ European reference populations??

[Leo76]

Still haven't been able to find an answer to this anywhere, and Geno/FTDNA haven't been particularly helpful. In fact I'm still waiting for an answer of any kind from them.

The European reference populations in the "First Generation" of Geno 2.0 (Britain, Germany, etc) all reflected some degree of Mediterranean or Southwest Asian DNA. (This represented the genetic component of the Neolithic migration into Europe from peoples of the Near East, that most all modern Europeans share.)

The European reference populations of Geno 2.0+, however, completely lack any such admixtures. Gone. Poof. Abracadabra. Into thin air. This is the case in all of them: British, Irish, French, German, et al. With the occasional remotely conceivable exception of some "Southern Europe" or "Jewish Diaspora" admixtures, the actual Neolithic components are gone in every one. The Euro reference populations are now almost wholly "European", lacking the Neolithic admixture that is well known to be there. Why? Nat Geno has not explained this recalibration, and it's irking me.

The readjustment has not been minor, either, nor merely semantic. If you compare the respective populations in the two different tests (linked above), you'll see that even in cases of "Southern Europe" or "Jewish Diaspora" of Geno 2.0+, the actual percentage is FAR lower than the respective "Mediterranean" or "Southwest Asian" of Geno 2.0 First Gen.

Thoughts? This is bugging me because my Geno 2.0+ results show me as having 2% "Arabian" DNA (the rest is all purely European), but according to the new reference populations, this is exotic.

[wombat]

I think they just subsumed the proper amount into each of the new European categories. It wouldn't be possible to have constructed any of the new categories had they not.

[Leo76]

I think you're probably right.

But that makes no sense, and defeats the purpose of the Regional Ancestry feature in the first place.

If you're going to call British DNA just entirely "British" despite the fact that it consistently contains a measurable Near Eastern component, then why not, for hypothetical example, just call the DNA of every white person living in America just "European" and not bother with further regional admixture breakdowns? In other words, by "masking" the Near Eastern DNA this way, they're grossly oversimplifying.

Further, not all Europeans share the same degree of these Near Eastern admixtures. It's doing a disservice to genetically-European Geno customers to just suggest that we ALL carry x% Neolithic Near Eastern DNA. Some will have more, some will have less. So we deserve to see a breakout, I think.

Again, I think you're probably right, and one possible explanation may have to do with the fact that they've recalibrated the average European Near Eastern admixture, and it now consistently shows as less than 2%, which is their cutoff point for statistical noise and display in regional proportions. So my 2% "Arabian" admixture might have just peeked above the water line.

But then, it would have been nice if they had EXPLAINED this somewhere.

[wombat]

I think you're probably right.

But that makes no sense, and defeats the purpose of the Regional Ancestry feature in the first place.

If you're going to call British DNA just entirely "British" despite the fact that it consistently contains a measurable Near Eastern component, then why not, for hypothetical example, just call the DNA of every white person living in America just "European" and not bother with further regional admixture breakdowns? In other words, by "masking" the Near Eastern DNA this way, they're grossly oversimplifying.

Further, not all Europeans share the same degree of these Near Eastern admixtures. It's doing a disservice to genetically-European Geno customers to just suggest that we ALL carry x% Neolithic Near Eastern DNA. Some will have more, some will have less. So we deserve to see a breakout, I think.

Again, I think you're probably right, and one possible explanation may have to do with the fact that they've recalibrated the average European Near Eastern admixture, and it now consistently shows as less than 2%, which is their cutoff point for statistical noise and display in regional proportions. So my 2% "Arabian" admixture might have just peeked above the water line.

But then, it would have been nice if they had EXPLAINED this somewhere.

Well they don't just pretend nobody has any excess. I think they subsume as much as standard for each new European regional base component as need be. There is no other way to form such regional components otherwise, certainly not without getting confusing results where someone might get like 40% Mediterranean and Southwest Asian and 55% British & Irish when they are all British & Irish. And someone from Norway getting similar but with Scandinavian instead of so much British & Irish. I suppose, if they made that clear, it might be an interesting presentation and maybe manage to give more info at once. However, it's possible that it might not be easy to separate out ancient regional hunter-gather bits from that and form as stable of new components perhaps?

It just shows that there was worth in having tested on both versions. Each presents some interesting bits that one can't see on the other test.

Anyway you'll see that at places that take things even further and really one step it, like 23 don't show any hint at all of that farmer stuff. Ancestry and FTDNA do not either.

Here they present say Western and Central European, British & Irish, Eastern European, etc. as containing a certain mix of the ancient hunter-gather type of that region plus the two farmer migrations that form the basis for that component. You'll see some people still need excess farmer stuff on top of that, like look at French, Italians in particular and small bits for I think it was the British and say Russians, etc. In some of the reference populations overviews they give notes and tell you whether the excess farmer stuff for that reference population is thought to be ancient signal beyond which the main European regional components for that reference population contain or whether they are thought to be relatively more recent mixings from Southern Europe. If you are almost totally from one of the places they have a reference for but have much more than that might hint an actual recent ancestor from such a region.

[wombat]

I think maybe doing it this way helps make it a little clearer for those with a bit more mixed ancestry to try to pick some stuff out. If they dealt only with people who were very largely one thing and then maybe just one or two other similar things and trace something way different maybe they could have still done it a bit more in the old style but just broken the Northern European into British&Irish, Northern and Central, Scandinavian, Eastern European, etc. (again not 100% sure they could do that as stably or not).

[wombat]

For British & Irish it seems to be the signal of the ancient hunter-gatherers of that region plus the average amount of farmer stuff the Irish and Scottish had (thus the British still get a little bit of extra ancient added on outside on average).
Going by the previous test it seems that includes a bit less farmer stuff than the Western and Central European component would have built in and a bit more than the Scandinavian and Eastern European ones would.

[wombat]

What is your background? I'm guessing from somewhere in the U.K.?

[Leo76]

In some of the reference populations overviews they give notes and tell you whether the excess farmer stuff for that reference population is thought to be ancient signal beyond which the main European regional components for that reference population contain or whether they are thought to be relatively more recent mixings from Southern Europe.

Hmm, thanks for mentioning that. Will have to go back and look at those, because I didn't look at any Euro pops. that aren't far NW European.

[Leo76]

What is your background? I'm guessing from somewhere in the U.K.?

All my family has been in America a looong time (since before 1770, on all branches), but yes, mainly UK, with some French and German.

My Geno 2.0+ breakdown is:

Britain and Ireland: 52%
Western and Central Europe: 31%
Scandinavia: 14%
Arabia: 2%

Or, more easily visualized:

http://i.imgur.com/ctqrRIS.jpg

[wombat]

All my family has been in America a looong time (since before 1770, on all branches), but yes, mainly UK, with some French and German.

My Geno 2.0+ breakdown is:

Britain and Ireland: 52%
Western and Central Europe: 31%
Scandinavia: 14%
Arabia: 2%

Or, more easily visualized:

http://i.imgur.com/ctqrRIS.jpg

I guess those seem pretty reasonable then.

My dad gets 88% Eastern European and 12% Finnish & Siberian. It seems like Baltic people don't come remotely close to any of their reference populations, they seem to get so much Eastern European so purely compared to basically everyone else.
He got 87% EE here before phasing and 80% after. He also gets 2% Finnish here and a trace Balkan and a fraction of British & Irish and some Broadly European and touch of Broadly Northwestern European.

His known ancestry is so far tracked all Latvian (with rumors that one line might go to Polish).

Going by results here and the two Geno tests it seems like in addition to the Latvian he must have some Finnish ancestor in genealogical time frame (since he both has some 100% Finnish matches here and a trace Finnish survives even in Conservative mode and his Finnish & Siberian seems to be larger than normal for Baltics on the other test and on the earlier version of that other test there are signs that he has some sort of Finnish-like component balancing out some sort of component from the vaguely eastern Romanian type region) and also one from somewhere down south more in the general eastern Hungary, eastern Romania, eastern Balkan, Western Ukraine or some such.

[wombat]

Combining his Geno 2.0 and Geno 2.0 NG results actually places him more directly than 23 does since they pretty end up signally out that there must be a lot of Baltic while the 23 would basically leave it up in the air where in their huge Eastern European region he'd fall.

[Georgeanna7]

Significant Discrepancies

This conversation has been a tremendous in helping me to begin to sort out the significant discrepancies between my Gen 2.0 and Gen 2.0 NG results. With all other regions being comparable in both tests, (in 2.0 ) I went from 10 % Mediterranean with 4% Southwest Asian to (in 2.0+) 13% Scandinavian. The search and the research continues. Thanks for sharing.

[Leo76]

Glad this thread was in some way a help in you not feeling so alone, Georgeanna.

I'm sure there's some logical explanation for why the company made the Mediterranean and Southwest Asian admixtures "disappear" with the new test (perhaps, as wombat suggests, they just proportionally absorbed them into the profiles of each regional European population), but I just wish they had EXPLAINED that and ARTICULATED their methodology!!!

[Georgeanna7]

Mediterranean to Scandinavian=Scandalous

I don't know Leo76. That is a heck of a lot of subsuming! It is akin to "turning adipose tissue into muscle tissue". It is a physiological impossibility. One replaces the other. In this case, at least with my results, Scandinavian has completely replaced Mediterranean. The only logical explanation would be - what they thought was Mediterranean in Gen 2.0 should have actually been attributed to Scandinavia; a "contribution or deposit" of the Vikings raids that went into North African and Mediterranean. Still, as you stated, they should have given an explanation. I am still learning...

[Leo76]

That is a heck of a lot of subsuming! It is akin to "turning adipose tissue into muscle tissue".

Yeah, I was just giving wombat's hypothesis the fairest possible shake. It doesn't make much sense, does it.

In my case, the first version of the test (Geno 2.0) had me at 38% Mediterranean and 17% SW Asian, for a total of 55% vaguely "near Eastern" origin. (The rest--the majority--was Northern Europe. Those combined admixtures matched almost perfectly with the same components in the German reference population at the time.) With the second version of the test (Geno 2.0+), ALL OF THAT is gone in my results, with the exception of a 2% "Arabian" component.

My results in Geno 2.0+ are now:

Great Britain and Ireland: 52%
Western and Central Europe: 32%
Scandinavia: 14%
Arabia: 2%

This makes MUCH more sense given my known ancestry, but again, it doesn't explain the huge divergence between Geno 2.0 and 2.0+. I'm starting to think more and more that they were just REALLY way off on Geno 2.0 and are just trying to "gloss over it" now. Hence the lack of communication and explanation.

Kind of like, "Oh hey, you know all that DNA we thought was from SW Asia and the Mediterranean? Yeah, turns out it was native European all along, almost in its entirety. Let's COMPLETELY recalibrate the new test, LOL."