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

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

    New article in "Nature"

    http://www.nature.com/nature/journal...ture13673.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?

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    And where are Indo-Europeans in all of this? Looks like they are hidden under the name "ancient north Eurasians".

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    Quote Originally Posted by Tomenable View Post
    And where are Indo-Europeans in all of this? Looks like they are hidden under the name "ancient north Eurasians".
    "ancient north Eurasian" peak among Burusho and Caucasus people
    http://www.eupedia.com/forum/threads...rthern-Eurasia

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    We've been discussing Lazaridis et al on this Board for months. Just use the search engine...43 threads pop up.

    This is just one of them:
    http://www.eupedia.com/forum/threads...ight=Lazaridis


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    Quote Originally Posted by Angela View Post
    We've been discussing Lazaridis et al on this Board for months. Just use the search engine...43 threads pop up.

    This is just one of them:
    http://www.eupedia.com/forum/threads...ight=Lazaridis
    Yes - the previous paper. This is from this month, and seems to have something new, about a "basal Eurasian population".

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    Quote Originally Posted by Grubbe View Post
    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.

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    1 members found this post helpful.
    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/s...1/001552-3.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.

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    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
    có che un pòpoło no 'l defende pi ła só łéngua el xe prónto par èser s'ciavo

    when a people no longer dares to defend its language it is ripe for slavery.

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    Quote Originally Posted by Angela View Post
    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/s...1/001552-3.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?

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    Quote Originally Posted by Grubbe View Post
    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/-YbYK8NzQNA...1600/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/threads...=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. )

    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.

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    1 members found this post helpful.
    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.

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    Quote Originally Posted by Angela View Post

    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/threads...=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. )

    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.
    Be wary of people who tend to glorify the past, underestimate the present, and demonize the future.

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    Quote Originally Posted by LeBrok View Post
    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.

    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.)

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    Quote Originally Posted by Aberdeen View Post
    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.

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    Quote Originally Posted by Angela View Post
    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."

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    Quote Originally Posted by Angela View Post
    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.

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    Quote Originally Posted by Angela View Post
    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!

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    Quote Originally Posted by Aberdeen View Post
    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.

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    Quote Originally Posted by Grubbe View Post
    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/reic...Ancestries.pdf

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    Quote Originally Posted by Angela View Post
    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/reic...Ancestries.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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    Quote Originally Posted by Angela View Post
    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.
    Have they found other archaic admixture in Africans, that non-Africans don't have? Because they still haven't found any Neanderthal or Denisovan DNA in Africans?

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    Quote Originally Posted by Grubbe View Post
    Have they found other archaic admixture in Africans, that non-Africans don't have? Because they still haven't found any Neanderthal or Denisovan DNA in Africans?
    I don't want to de-rail this thread, so I would just suggest going to dienekes.blogspot.com and using the search engine there. It's pretty inactive now, but it has a great and well organized archive. I remember a lot of papers and posts there discussing archaic admixture in Africa.

    These are just two:

    http://dienekes.blogspot.com/2014/06...ixture-in.html

    http://dienekes.blogspot.com/2012/07...ixture-in.html


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    Quote Originally Posted by LeBrok View Post
    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%.
    Totally different? I would doubt that is frequently the case. The overlap in terms of the remaining Neanderthal genes even between Europeans and East Asians is marked, even though our lineages diverged tens of thousands of years ago.

    It also means that this surviving 29% of Neanderthal DNA is completely interchangeable and compatible with Sapiens DNA
    That isn’t at all my reading of Sankararaman et al (The authors included Paabo, Patterson and Reich)

    The genomic landscape of Neanderthal ancestry in present-day humans

    http://www.nature.com/nature/journal...ture12961.html

    “Regions that harbour a high frequency of Neanderthal alleles are enriched for genes affecting keratin filaments, suggesting that Neanderthal alleles may have helped modern humans to adapt to non-African environments. We identify multiple Neanderthal-derived alleles that confer risk for disease, suggesting that Neanderthal alleles continue to shape human biology.”

    Not all the negatively adaptive Neanderthal alleles have been ejected through purifying selection. If they had been, they wouldn’t continue to shape human biology through diseases like diabetes, lupus, cirrhosis, Crohn’s disease, and according to some studies, rheumatoid arthritis, Hepatitis C, small cell lung cancer, various heart and circulatory ailments, neurological disorders, long term depression etc.

    Future papers may paint a different story, but this seems to be the latest research on the subject, and it doesn’t seem to be very controversial.

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    1 members found this post helpful.
    Quote Originally Posted by Angela View Post

    Totally different? I would doubt that is frequently the case. The overlap in terms of the remaining Neanderthal genes even between Europeans and East Asians is marked, even though our lineages diverged tens of thousands of years ago. That isn’t at all my reading of Sankararaman et al (The authors included Paabo, Patterson and Reich)
    I can't find the study at the moment but this is the article that claims that, with name of lead research and University.
    http://www.livescience.com/42933-hum...hal-genes.html


    “Regions that harbour a high frequency of Neanderthal alleles are enriched for genes affecting keratin filaments

    suggesting that Neanderthal alleles may have helped modern humans to adapt to non-African environments. We identify multiple Neanderthal-derived alleles that confer risk for disease, suggesting that Neanderthal alleles continue to shape human biology.”

    Not all the negatively adaptive Neanderthal alleles have been ejected through purifying selection. If they had been, they wouldn’t continue to shape human biology through diseases like diabetes, lupus, cirrhosis, Crohn’s disease, and according to some studies, rheumatoid arthritis, Hepatitis C, small cell lung cancer, various heart and circulatory ailments, neurological disorders, long term depression etc.
    In all these cases probability of disease is rising especially in older age, but they are not eminent. Considering length of human life in the past, these maladies carrying genes were not that destructive. Otherwise they would have been weeded out already. We are just "unlucky" to live too long, and experience full Neanderthal heritage. ;)

    In complicated systems or organisms as humans, many genes have dual or multiple functions. Increase risk for a certain disease is compensated by beneficial action on behave of organs or systems. Sickle cell anemia pops as fast example.
    So perhaps these increased predispositions to sickness inherited from Neanderthal might be compensated by better adaptation to cold and new diet, from action of same genes.
    Last edited by LeBrok; 26-09-14 at 18:33.

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    Quote Originally Posted by Angela View Post
    I don't want to de-rail this thread, so I would just suggest going to dienekes.blogspot.com and using the search engine there. It's pretty inactive now, but it has a great and well organized archive. I remember a lot of papers and posts there discussing archaic admixture in Africa.

    These are just two:

    http://dienekes.blogspot.com/2014/06...ixture-in.html

    http://dienekes.blogspot.com/2012/07...ixture-in.html
    Thanks again.

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