Ancient human genomes suggest three ancestral populations for present-day Europeans

Grubbe

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New article in "Nature"

http://www.nature.com/nature/journal/v513/n7518/full/nature13673.html

"We sequenced the genomes of a ~7,000-year-old farmer from Germany and eight ~8,000-year-old hunter-gatherers from Luxembourg and Sweden. We analysed these and other ancient genomes with 2,345 contemporary humans to show that most present-day Europeans derive from at least three highly differentiated populations: west European hunter-gatherers, who contributed ancestry to all Europeans but not to Near Easterners; ancient north Eurasians related to Upper Palaeolithic Siberians, who contributed to both Europeans and Near Easterners; and early European farmers, who were mainly of Near Eastern origin but also harboured west European hunter-gatherer related ancestry. We model these populations’ deep relationships and show that early European farmers had ~44% ancestry from a ‘basal Eurasian’ population that split before the diversification of other non-African lineages."

Has anyone read the full text yet?
 
And where are Indo-Europeans in all of this? Looks like they are hidden under the name "ancient north Eurasians".
 
Yes - the previous paper. This is from this month, and seems to have something new, about a "basal Eurasian population".

Basal Eurasian was discussed in the pre-print.
 
Sorry, that was a little abrupt...I was in a bit of a rush. :)

It was discussed in the Supplementary Info portion (which is the guts of their analysis) of the preprint, in the section written by Lazaridis, Patterson and Reich.

This is the link:
http://biorxiv.org/content/biorxiv/suppl/2013/12/23/001552.DC1/001552-3.pdf

For some reason, it just wasn't discussed very much here.

There's been all sorts of speculation about it, with some internet posters proposing that it was a component created by the addition of subsequent African gene flow into the Middle East, perhaps through the Natufians. That's clearly incorrect if the authors are getting it right, as their model indicates that the component existed prior to the split of all the other homo sapiens sapiens lineages.

Others have proposed that it is somehow more African, perhaps because they are assuming that it was the first group to leave Africa, and so it would have evolved less than the others? I don't think that follows, however. I would think it would indeed have evolved, and that all human lineages evolve, although they may evolve differently. I think it's more probable that the differences stem from the fact that they were more isolated.

The real puzzle to me is where were they located that they could escape admixture with other human lineages for so long?

I think I read some post that posits that the difference is Neanderthal heritage. I haven't thought it through completely, but I think that's a possibility that should be explored. Again, though, where were they hiding that they avoided it?

Ed.I think it's important to realize that these are models as the authors keep on pointing out. As more ancient genomes are analyzed the models may change. They are very precise in their language. As just an example, they say that most Europeans can be modeled as mixtures of at least these three ancestral populations. That leaves room for others. Also, if we finally get samples from the Near East or even from the North Mediterranean Mesolithic, things may become clearer and more detailed models may be produced.
 
Further to the above...Last week...Mr. Reich moved Stuttgart model away from the Sardinian group and into the bergamo group ...............unsure if this movement meant away also from basque and iberian and more into central european/ upper danubian block
 
Sorry, that was a little abrupt...I was in a bit of a rush. :)

It was discussed in the Supplementary Info portion (which is the guts of their analysis) of the preprint, in the section written by Lazaridis, Patterson and Reich.

This is the link:
http://biorxiv.org/content/biorxiv/suppl/2013/12/23/001552.DC1/001552-3.pdf

For some reason, it just wasn't discussed very much here.

There's been all sorts of speculation about it, with some internet posters proposing that it was a component created by the addition of subsequent African gene flow into the Middle East, perhaps through the Natufians. That's clearly incorrect if the authors are getting it right, as their model indicates that the component existed prior to the split of all the other homo sapiens sapiens lineages.

Others have proposed that it is somehow more African, perhaps because they are assuming that it was the first group to leave Africa, and so it would have evolved less than the others? I don't think that follows, however. I would think it would indeed have evolved, and that all human lineages evolve, although they may evolve differently. I think it's more probable that the differences stem from the fact that they were more isolated.

The real puzzle to me is where were they located that they could escape admixture with other human lineages for so long?

I think I read some post that posits that the difference is Neanderthal heritage. I haven't thought it through completely, but I think that's a possibility that should be explored. Again, though, where were they hiding that they avoided it?

Ed.I think it's important to realize that these are models as the authors keep on pointing out. As more ancient genomes are analyzed the models may change. They are very precise in their language. As just an example, they say that most Europeans can be modeled as mixtures of at least these three ancestral populations. That leaves room for others. Also, if we finally get samples from the Near East or even from the North Mediterranean Mesolithic, things may become clearer and more detailed models may be produced.


OK, thanks. I really haven't read the full Supplementary info before, only bits and pieces. If I had, I would have clearly seen that the Basal Eurasians were discussed.

What made it so confusing, is that not only has the Basal Eurasians not been discussed at any lenght in this forum, but not in other forums I visit either - before now. And it is also only now that the press has started writing about it. Seems they didn't read the full Supplementary info before either ;)

If I understand it correctly, at least a few populations haven't any Basal Eurasian DNA, for instance (or only?) the Karitina. And those populations which have Basal Eurasian DNA, have got it through "Stuttgart", who got it though "The Near East". So perhaps these Basal Eurasians hid somewhere in or around the Near East? But why didn't the Karitina get anything? Were they busy running away eastwards before the remaining(?) people near Africa found these Basal Eurasians and mingled with them? Or have I misunderstood something?
 
OK, thanks. I really haven't read the full Supplementary info before, only bits and pieces. If I had, I would have clearly seen that the Basal Eurasians were discussed.

What made it so confusing, is that not only has the Basal Eurasians not been discussed at any lenght in this forum, but not in other forums I visit either - before now. And it is also only now that the press has started writing about it. Seems they didn't read the full Supplementary info before either ;)

If I understand it correctly, at least a few populations haven't any Basal Eurasian DNA, for instance (or only?) the Karitina. And those populations which have Basal Eurasian DNA, have got it through "Stuttgart", who got it though "The Near East". So perhaps these Basal Eurasians hid somewhere in or around the Near East? But why didn't the Karitina get anything? Were they busy running away eastwards before the remaining(?) people near Africa found these Basal Eurasians and mingled with them? Or have I misunderstood something?


You might want to try the Anthrogenica forum, as it's been discussed on that Board...usually in the context of the experiments being conducted using some of this new software, however.

Also, to refresh our recollections, this is their final model in that paper, although I'm sure it won't be the final model.
http://3.bp.blogspot.com/-YbYK8NzQNAY/UrihRsR5eSI/AAAAAAAAJbo/TYynaV4cO4Y/s1600/model.png

So far as I understand it, the prevailing theory is that Europeans got it through Stuttgart like people. As to where the Stuttgart like EEFs got it the prevailing theory has been that it was in the Near East, which makes sense as all modern Near Easterners have EEF As I said, that doesn't seem like an isolated enough area to me for them to have avoided admixture with all of the other Out of Africa lineages for so long, unless there were physical barriers of some sort...water...desert...mountains...

Perhaps Arabia is a good choice. The bottom line is that I don't know and neither does anyone else as of yet.

A poster at Anthrogenica named Parasar has come up with a provocative theory that they were actually in southern Mediterranean Europe. I haven't thought that one through either, and I have no idea if it's correct. These ideas can be posited because we have, as yet, no idea what these southern hunter gatherers were like. (the ones from Greece, the Balkans, perhaps the now submerged lands of the Adriatic where Italy and the Balkans meet.

Someone (perhaps the same poster?), proposed that maybe it was just that the Basal Eurasians are the Eurasians who didn't mix with Neanderthas. I haven't followed the data on the locations of presumed Neanderthal admixture closely enough to say whether that's supported by the evidence. I will, say, however, that I don't believe that the development of agriculture, and later metallurgy, happened in the Near East just because they were blessed with a great climate and fauna and floral at an opportune time. Human genetic structure is not only influenced by the environment, in my view, which pushes evolution along certain lines, but rather, the genetic composition of certain groups also changes the environment and indeed culture.

I am not, as you can probably tell, a fan of the admixture between Neanderthals and Homo Sapiens Sapiens. While I don't think Neanderthals were the total brutes of the popular imagination of prior times, if the results of the admixture with them is summed out, I think we lost by it. In return for some bone and skin adaptations for cold weather, we got a whole raft of debilitating and sometimes deadly autoimmune disorders, mental disorders, and, in my opinion, some diminution of higher level cognitive function. There have been some recent papers that have discussed this issue. You can find them in this thread here:
http://www.eupedia.com/forum/thread...y-of-the-Neanderthals?highlight=Neanderthals-

(If you read it you will see that we had quite a spirited debate, and I was unable to persuade everyone to the "correct" view.
grin.png
)

I've also been looking at the abstracts of a conference just held in Florence on evolution, and found the abstract of a paper called The Higher Cognitive Functions of the Recently Expanded Parietal Lobes of Homo Sapiens (versus Neanderthals) by Frederick Coolidge. He maintains that recent research shows that this difference in brain structure manifests itself in terms of working memory, numerosity and abstract thinking, episodic memory, progressive memory, sense of self, among others.

I'd be happy to post it and others of interest here, but my attachment function won't permit it.
 
If Neanderthal DNA was responsible for all kinds of genetically based health issues, mental health issues and lower cognitive functions, I'd expect Sub-Saharan Africans to be free from all those issues, but that's not the case. There are some differences in prevalence of specific health issues among different races, but that's a different issue, IMO. Not having Neanderthal DNA doesn't make a particular group superior, on average, to those who do have Neanderthal DNA.

As for basal Euopeans, I'll believe in them when I meet some. Although, if they did exist, Arabia might seem like a good place for an isolated population. Unless, back in the relevant time period, Arabia was fertile grassland instead of the desert it later became.
 
I am not, as you can probably tell, a fan of the admixture between Neanderthals and Homo Sapiens Sapiens. While I don't think Neanderthals were the total brutes of the popular imagination of prior times, if the results of the admixture with them is summed out, I think we lost by it. In return for some bone and skin adaptations for cold weather, we got a whole raft of debilitating and sometimes deadly autoimmune disorders, mental disorders, and, in my opinion, some diminution of higher level cognitive function. There have been some recent papers that have discussed this issue. You can find them in this thread here:
http://www.eupedia.com/forum/thread...y-of-the-Neanderthals?highlight=Neanderthals-

(If you read it you will see that we had quite a spirited debate, and I was unable to persuade everyone to the "correct" view.
grin.png
)

I've also been looking at the abstracts of a conference just held in Florence on evolution, and found the abstract of a paper called The Higher Cognitive Functions of the Recently Expanded Parietal Lobes of Homo Sapiens (versus Neanderthals) by Frederick Coolidge. He maintains that recent research shows that this difference in brain structure manifests itself in terms of working memory, numerosity and abstract thinking, episodic memory, progressive memory, sense of self, among others.

I'd be happy to post it and others of interest here, but my attachment function won't permit it.
It is one way of looking at this, the other would be: if not Neanderthal admixture there wouldn't be Europe's, most Asians and Amerindians. 70 k years might not be long enough for out of Africa Sapiens to develop white skin and move North. 7 billion individuals in every corner of this planet is quite a feat, by measure of species success, and in spite of few diseases we picked up during mixing.

I've also been looking at the abstracts of a conference just held in Florence on evolution, and found the abstract of a paper called The Higher Cognitive Functions of the Recently Expanded Parietal Lobes of Homo Sapiens (versus Neanderthals) by Frederick Coolidge. He maintains that recent research shows that this difference in brain structure manifests itself in terms of working memory, numerosity and abstract thinking, episodic memory, progressive memory, sense of self, among others.
I'm sure this part of Neanderthal was weeded out from human genom. Nothing to worry about. Natural selection did the trick.
 
It is one way of looking at this, the other would be: if not Neanderthal admixture there wouldn't be Europe's, most Asians and Amerindians. 70 k years might not be long enough for out of Africa Sapiens to develop white skin and move North. 7 billion individuals in every corner of this planet is quite a feat, by measure of species success, and in spite of few diseases we picked up during mixing.

I'm sure this part of Neanderthal was weeded out from human genome. Nothing to worry about. Natural selection did the trick.

Perhaps, although I'm not totally convinced based on some of the people with whom I have to interact. :grin:

It might also have been different 12,000 years ago.

(Not to flog a dead horse, but the de-pigmentation snps possessed by the Neanderthals are not, to the best of my recollection, the ones present in Europeans. There's some posts on the Board about it.)
 
If Neanderthal DNA was responsible for all kinds of genetically based health issues, mental health issues and lower cognitive functions, I'd expect Sub-Saharan Africans to be free from all those issues, but that's not the case. There are some differences in prevalence of specific health issues among different races, but that's a different issue, IMO. Not having Neanderthal DNA doesn't make a particular group superior, on average, to those who do have Neanderthal DNA.

I don't know if I would put it as starkly as all that. Plus, we all now have Neanderthal or other 'archaic' admixture. It's a human issue, imo, not one group of us versus another. I hasten to add that in terms of "Basal" versus other non-African lineages, it's only one speculation among many.

Anyway... the way you view Neanderthal admixture all depends on how you interpret the latest papers.

This is the link to the Svante Paabo, Patterson and Reich paper: http://www.nature.com/nature/journal...ture12961.html

It's not open access, but the tables and supplementary information are available at the links below.
http://www.nature.com/nature/journal...#extended-data

http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature12961-s1.pdf


This is a link to the Vernot et al paper, which is also restricted access:
http://www.sciencemag.org/content/ea...cience.1245938

The link for the supplementary information can be found below.
http://www.sciencemag.org/content/su.../Vernot.SM.pdf

Dienekes discusses them here:http://www.dienekes.blogspot.com/201...rn-humans.html

http://www.dienekes.blogspot.com/2014/01/resurrecting-neandertal-lineages-vernot.html


As for basal Euopeans, I'll believe in them when I meet some. Although, if they did exist, Arabia might seem like a good place for an isolated population. Unless, back in the relevant time period, Arabia was fertile grassland instead of the desert it later became.

I do like your turn of phrase.:) I'm not totally comfortable with these "ghost" populations either, although to be fair, the ANE group were a "ghost" population discovered through mathematical modeling long before their existence was confirmed through the analysis of the Mal'ta genome.
 
I don't know if I would put it as starkly as all that. Plus, we all now have Neanderthal or other 'archaic' admixture. It's a human issue, imo, not one group of us versus another. I hasten to add that in terms of "Basal" versus other non-African lineages, it's only one speculation among many.

Anyway... the way you view Neanderthal admixture all depends on how you interpret the latest papers.

This is the link to the Svante Paabo, Patterson and Reich paper: http://www.nature.com/nature/journal...ture12961.html

It's not open access, but the tables and supplementary information are available at the links below.
http://www.nature.com/nature/journal...#extended-data

http://www.nature.com/nature/journal/vaop/ncurrent/extref/nature12961-s1.pdf


This is a link to the Vernot et al paper, which is also restricted access:
http://www.sciencemag.org/content/ea...cience.1245938

The link for the supplementary information can be found below.
http://www.sciencemag.org/content/su.../Vernot.SM.pdf

Dienekes discusses them here:http://www.dienekes.blogspot.com/201...rn-humans.html

http://www.dienekes.blogspot.com/2014/01/resurrecting-neandertal-lineages-vernot.html




I do like your turn of phrase.:) I'm not totally comfortable with these "ghost" populations either, although to be fair, the ANE group were a "ghost" population discovered through mathematical modeling long before their existence was confirmed through the analysis of the Mal'ta genome.

Fair enough. I suppose that if someone does manage to find those basal Europeans, those who believed in the idea will seem as if they're a lot smarter than the sceptics.

As for our Neanderthal genetic inheritance, it seems as if the scientific concensus is changing quickly. I look forward to seeing people wearing T-shirts that say "My ancestors were Neanderthals and all I got out of it was a neurological disease."
 
Perhaps, although I'm not totally convinced based on some of the people with whom I have to interact.
lol

(Not to flog a dead horse, but the de-pigmentation snps possessed by the Neanderthals are not, to the best of my recollection, the ones present in Europeans. There's some posts on the Board about it.)
Possibly due to further mutations, thus depigmentation snps not matching neanderthal ones exactly anymore.
 
You might want to try the Anthrogenica forum, as it's been discussed on that Board...usually in the context of the experiments being conducted using some of this new software, however.

Yes, I will try the Anthrogenica forum. Thanks!
 
If Neanderthal DNA was responsible for all kinds of genetically based health issues, mental health issues and lower cognitive functions, I'd expect Sub-Saharan Africans to be free from all those issues, but that's not the case. There are some differences in prevalence of specific health issues among different races, but that's a different issue, IMO. Not having Neanderthal DNA doesn't make a particular group superior, on average, to those who do have Neanderthal DNA.

I definitely agree.
 
I definitely agree.

Since all homo sapiens sapiens now have either Neanderthal or other archaic admixture it is, imo, and as I said upthread, a "human" issue, not an "ethnic" one.

Since we've been discussing Lazaridis et al, here is a quote from the paper:
"The ancient individuals had indistinguishable levels of Neanderthal ancestry when compared to each other (,
2%) and to
of Neanderthal ancestry when compared to each other (
,
2%) and to
present-dayEurasians."

http://genetics.med.harvard.edu/rei...14_Nature_Lazaridis_EuropeThreeAncestries.pdf
 
Since all homo sapiens sapiens now have either Neanderthal or other archaic admixture it is, imo, and as I said upthread, a "human" issue, not an "ethnic" one.

Since we've been discussing Lazaridis et al, here is a quote from the paper:
"The ancient individuals had indistinguishable levels of Neanderthal ancestry when compared to each other (,
2%) and to
of Neanderthal ancestry when compared to each other (
,
2%) and to
present-dayEurasians."

http://genetics.med.harvard.edu/rei...14_Nature_Lazaridis_EuropeThreeAncestries.pdf

The amount of whole Neanderthal genome floating around is about 20%. It means that my 2% of Neanderthal might be totally different from next person's 2%. It also means that this surviving 20% of Neanderthal DNA is completely interchangeable and compatible with Sapiens DNA
 

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