The genetic history of Ice Age Europe

[epoch]

@Angela

The paper also suggest something Mal'ta related for the Middle-Eastern affinity.

All three of the best fitting models in Extended Data Figure 4 specify that the majority ancestry component in Satsurblia branched very deeply in the tree of West Eurasian populations, forming a clade with Malta1

 

[Fire Haired14]

Look what happens when you place Vestonice16(30ky Central Europe), Villabruna, Kostinki14, Anatolia_Neolithic, CHG, and Afontova Gora3(Younger version of MA1) in a tree with East Asians and Africans and allow there to be 4 or 5 admixture events.

4 admixture events
5 admixture events.

4admixture events:
Mixed populations.

PC4	Basal Eurasian	Basal WHG	Basal ANE	East Asian
CHG
EEF/Anatolia Neolithic
Villabruna
Dai/Han

[TD="align: right"]33[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]67[/TD]
[TD="align: right"]0[/TD]

[TD="align: right"]64[/TD]
[TD="align: right"]46[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]

[TD="align: right"]0[/TD]
[TD="align: right"]66[/TD]
[TD="align: right"]44[/TD]
[TD="align: right"]0[/TD]

[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]11[/TD]
[TD="align: right"]89[/TD]

5 admixture events

PC5	Basal West Eurasian	Basal WHG	Basal ANE	East Asian	Basal Kostinki
CHG
EEF/Anatolia Neolithic
Villabruna
Dai/Han
Ust ishim

[TD="align: right"]56[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]44[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]

[TD="align: right"]72[/TD]
[TD="align: right"]28[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]

[TD="align: right"]0[/TD]
[TD="align: right"]57[/TD]
[TD="align: right"]43[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]

[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]37[/TD]
[TD="align: right"]63[/TD]
[TD="align: right"]0[/TD]

[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]75[/TD]
[TD="align: right"]25[/TD]

5 admixture events with MA1 included.

PC6	Basal West Eurasian	Basal WHG	Very Basal ANE	Basal ANE	East Asian	Basal CHG
CHG
EEF/Anatolia Neolithic
Villabruna
Dai/Han

[TD="align: right"]87[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]13[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]

[TD="align: right"]73[/TD]
[TD="align: right"]27[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]

[TD="align: right"]0[/TD]
[TD="align: right"]62[/TD]
[TD="align: right"]38[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]5[/TD]

[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]0[/TD]
[TD="align: right"]12[/TD]
[TD="align: right"]88[/TD]
[TD="align: right"]0[/TD]

 

[epoch]

Wow. That last one. What is the difference between Basal ANE and Very Basal ANE?

 

[bicicleur 2]

I suppose very basal ANE is Ma1
So all ANE in Villabruna is reduced to Ma1
Could EEF/Neolithic Anatolia have recieved West Eurasian from CHG without getting the ANE or do we have to look for a common source of West Eurasian for both EEF/Neolithic Anatolia and CHG ?

 

[Sile]

R1b would have been picked up by farmers in great numbers, the same way I2 was picked up from WHGs in Anatolia. So far all Neolithic samples from Balkans don't have R1b. If farmers EEF are from fertile crescent then R1b can't be. R1b probably just started showing up there after 7kya but not before.

Who says all EEF ( 100% ) is from the fertile crescent ?

The south caucasus would be ideal for farming in the same ancient period

The black, caspian and aral seas are all fresh water seas ideal for farming in ancient times....................even when the black sea eventually broke into the Med, there was still drinkable/farming water

 

[Angela]

I still haven't found the time to look at the stats carefully, but just some general thoughts.

Is it really probable that all the scientists at the two best population genetics labs in the world, with access to all the available ancient genomes, and most probably ones that have not yet been released, including people who created some of the programs that are being used, and with infinitely more computing power at their disposal, didn't look at Afontova Gora? Are we supposed to believe that because the tentative conclusions, or better, alternatives, proposed by these authors don't match the results of some experiments posted at Eurogenes these authors misunderstood their own stats?

I personally don't find it probable, especially since it seems that confusion apparently reigns over there, although I'll admit I just skimmed the posts. Of course, it's possible. For now, I'll go with what these labs propose, and wait to see whether further publications based on other ancient genomes clarify the situation.

One minor point, has it been investigated whether the relationship between Villabruna or any of the other IceAge Europeans could be explained not by the ANE but by any non ANE ancestry in Afontova Gora?

 

[epoch]

I still haven't found the time to look at the stats carefully, but just some general thoughts.

Is it really probable that all the scientists at the two best population genetics labs in the world, with access to all the available ancient genomes, and most probably ones that have not yet been released, including people who created some of the programs that are being used, and with infinitely more computing power at their disposal, didn't look at Afontova Gora? Are we supposed to believe that because the tentative conclusions, or better, alternatives, proposed by these authors don't match the results of some experiments posted at Eurogenes these authors misunderstood their own stats?

Call to authority.

FWIW: I think the D-stats differences between AG3 and Mal'ta, as well as the fact that AG3 is not high coverage made them cautious. But the paper itself already hints to it itself:

The only way to explain these patterns is a history of gene flow between the ancestors of eastern non-Africans on the one hand, and the ancestors of three groups:
(a) A subset of Villabruna Cluster samples
(b) Early European farmers
(c) Mal’ta Cluster.
Such gene flow would induce a negative bias in two key statistics highlighted in Seguin-Orlando et al.
Note that for this to explain the data, three separate gene flow events are not required. Supplementary Information section 11 and Figure 4b document a link between (a)
and (b), so as few as two gene flow events may be needed. Understanding the exact gene flow history responsible for these patterns is difficult with the ancient DNA sample series
available here, but is an important question to address in future work.

I personally don't find it probable, especially since it seems that confusion apparently reigns over there, although I'll admit I just skimmed the posts. Of course, it's possible. For now, I'll go with what these labs propose, and wait to see whether further publications based on other ancient genomes clarify the situation.

One minor point, has it been investigated whether the relationship between Villabruna or any of the other IceAge Europeans could be explained not by the ANE but by any non ANE ancestry in Afontova Gora?

Don't know. Davids threads have a lot of D-stats.

 

[holderlin]

One minor point, has it been investigated whether the relationship between Villabruna or any of the other IceAge Europeans could be explained not by the ANE but by any non ANE ancestry in Afontova Gora?

This is what i was thinking, and I believe that is what the stats are suggesting. The timing is right for the widespread appearance of Han alleles in euros too.

So far everything fits with WHG/ANE->CHG->ENF?

 

[Fire Haired14]

Wow. That last one. What is the difference between Basal ANE and Very Basal ANE?

Very Basal ANE broke off of the ANE branch earlier than Basal ANE. ANE in these trees is Afortgova, the earlier the branch that mixes into another sample the more basal form of ANE and less related to Afortgova it is.

 

[holderlin]

Dem D-stats. Seriously. Analysis is confounding with so many.

It reminds me of a pre-computer detective drama where they have a bulletin board with a web of strings connecting countless people.

"Sir the data suggests that JFK was killed by a young Jimmy Hendrix."

"He also had lots of ANE"

 

[MOESAN]

This touches on one aspect of the R1b argument imo - the people arguing aren't always talking about the same bit of R1b.

Right - and even for V88 I don't have too much confidence in some chronology calculations; have they found V88 on old skeletons in Chad????
someones say V88 formed in Iberia; the discussion seems still open...
Even if data is coming up, we still need more and more to be sure

 

[Angela]

epoch;479988]Call to authority.

Darn straight, Epoch. That's exactly what I did. If I may be so blunt, if I need medical advice for a serious issue I don't rely on some jamoke on the internet who doesn't post under his real name and whose qualifications I can't check, and who might also be somebody with an undisclosed and unsavory bias. I do an exhaustive search of a professional's education and other qualifications. If it's a doctor I find out how many malpractice suits have been filed against him or her. Not that I then just rely on them. I ultimately don't blindly trust anyone. It must be genetic. Just as I do here I do my own research and ask tough questions and challenge what they're saying until I'm satisfied I'm getting the best possible advice. It may not make me the ideal patient from their point of view, but that's too damn bad for them; if they don't like the color of my money I can go elsewhere. Of course, every once in a while there is an amateur who surprises everyone, including me...i.e. Gioiello!

FWIW: I think the D-stats differences between AG3 and Mal'ta, as well as the fact that AG3 is not high coverage made them cautious. But the paper itself already hints to it itself

A bald statement that "We also find no evidence for the suggestion that the Mal'ta lineage contributed to Upper Paleolithic Europeans..." doesn't sound like they're waffling to me. It sounds pretty darn definite. However, maybe you're correct and it is because they are being cautious because AG3 is so low coverage. By the same token, if it's so low coverage that scientists are unwilling to use it, then should anyone be drawing such vast conclusions based on it? Has anyone thought to contact the lead author and ask about it? The few times I've done that they've been remarkably forthcoming. Maybe it is as simple as AG3 indeed being too low coverage. At least we'd know. Also, has it been checked whether the relationship between AG3 and Upper Paleolithic Europeans is necessarily because of shared ANE? Could it be AG3s other ancestry that is shared?

I just don't understand all this certainty when these experiments have so often led to wrong conclusions. I get even more skeptical when I read posts which make it clear there's still uncertainty about which populations should even be plugged into these programs.

Look, don't get me wrong. All I said is that I'm taking a wait and see attitude. Maybe some of these internet speculations will be proved to be correct, in which case mazel to everyone who picked up on it. I just think that we're not going to get clarity without ancient genomes from the Balkans, Anatolia, the Levant, and the areas around the Caucasus, genomes which the people at these labs may have already examined at least on a cursory level. The lead author here says she's been working on the genomes that are the subject of the paper for a few years.

 

[Greying Wanderer]

I suppose very basal ANE is Ma1
So all ANE in Villabruna is reduced to Ma1
Could EEF/Neolithic Anatolia have recieved West Eurasian from CHG without getting the ANE or do we have to look for a common source of West Eurasian for both EEF/Neolithic Anatolia and CHG ?

If the Caucasus acted as a barrier so CHG got ANE on its northern border but Anatolia only got the unmixed version on the southern border maybe? Or some kind of timing thing?

 

[Angela]

Dem D-stats. Seriously. Analysis is confounding with so many.

It reminds me of a pre-computer detective drama where they have a bulletin board with a web of strings connecting countless people.

"Sir the data suggests that JFK was killed by a young Jimmy Hendrix."

"He also had lots of ANE"

:grin::grin::grin: Good one! Sometimes they still use stickies on the bulletin boards, with magic marker lines going every which way...it's a you know what nightmare!

 

[APO276]

1b would have been picked up by farmers in great numbers, the same way I2 was picked up from WHGs in Anatolia. So far all Neolithic samples from Balkans don't have R1b. If farmers EEF are from fertile crescent then R1b can't be. R1b probably just started showing up there after 7kya but not before.

How many Neolithic samples from Balkans do we have? Is there a list somewhere?

 

[Alan]

I think this "Basal ANE" (what the heck is the difference between very Basal and just Basal??) of Eurogenes is basically a South_Central Asian component that as I said moved into the Caucasus via the Iranian Plateau, the Steppes via East of the Caspian and since the "Odd" ancetry in Villabruna resembles mostly the non Basal Eurasian ancestry in CHG, it probably also came via the Iranian Plateau-Caucasus route imo.

 

[LeBrok]

Look, don't get me wrong. All I said is that I'm taking a wait and see attitude. Maybe some of these internet speculations will be proved to be correct, in which case mazel to everyone who picked up on it. I just think that we're not going to get clarity without ancient genomes from the Balkans, Anatolia, the Levant, and the areas around the Caucasus, genomes which the people at these labs may have already examined at least on a cursory level. The lead author here says she's been working on the genomes that are the subject of the paper for a few years.

My sentiment too. I love speculation and I'm there with my predictions, but admittedly it is all of low certainty at the moment. There is no other way around, but to wait for more samples to see how balls fall to correct holes.

 

[Fire Haired14]

@Angela,

Most of what posters online are saying about these ancient genomes will turn out correct. They have the same tools academics do, so they're just as reliable.

My sentiment too. I love speculation and I'm there with my predictions, but admittedly it is all of low certainty at the moment. There is no other way around, but to wait for more samples to see how balls fall to correct holes.

We have a good collection. All the pieces are coming together. We just need ancient genomes from Southern Europe and Baltic/Finland/Russia to get the final details about the genetic origins of Europeans. It's incredible how much we've learned.

 

[LeBrok]

@Angela,

Most of what posters online are saying about these ancient genomes will turn out correct. They have the same tools academics do, so they're just as reliable.



We have a good collection. All the pieces are coming together. We just need ancient genomes from Southern Europe and Baltic/Finland/Russia to get the final details about the genetic origins of Europeans. It's incredible how much we've learned.

Yes, I like the progress and knowledge we achieved already. We also need many Near and Middle Eastern groups, the pure ENF (Natufian I suppose), the Basal Near Eastern - wherever he was hiding, need to check North Africa what was happening there and effect on WHG through Spain, and find pure Semitic one somewhere. Although the last one not important to Mesolithic and Neolithic Europe I guess. Still lots to do.

 

[epoch]

If the Caucasus acted as a barrier so CHG got ANE on its northern border but Anatolia only got the unmixed version on the southern border maybe? Or some kind of timing thing?

It did have quite an ice pack during LGM, so it wasn't easily traversable.