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Thread: How many population groups are there in terms of genetics?

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    Quote Originally Posted by parasar View Post
    On this point, I saw an interesting post at Eurogenes:
    http://eurogenes.blogspot.com/2016/0...b-saharan.html
    "When compared to non-African populations, FST measured at our integrated set of SNPs is relatively low between many groups from West, Central, and East Africa (yellows on the upper right triangle), whereas TVD in the same populations can reveal haplotypic differences as strong as between Europe and Asia"
    Yes, I plan to make a post about this at my blog. Way I grasp is that because groups like the "Khoisan" and various other African populations have had relatively higher population sizes throughout early Human pre-history when compared to Eurasians- :

     


    -this makes judging them by Fst a bit useless. Even between the Khoisan and Niger-Congo speakers like the Yoruba, Fst values aren't that high when compared to the Fst between Yorubas and East Asians:

     


    But I'd sooner group Yorubas in a "node" with Eurasians to the exclusion of the Khoisan than the other way around. For various African populations, Fst, which measures differences in allele frequencies, is not as useful for measuring divergence as it is for Eurasian / Out-of-Africa populations who've suffered through lower population sizes (or dips like the "Eurasian bottle-neck") in early Human pre-history which were more conducive to genetic drift. For the African groups Haplotypic differences and stuff like dating on Haplogroups is more relevant and in that case you will notice some pretty hefty divergences like the African element in Somalis looking like it's separated from Yorubas by about ~40,000 years. This is contradicted for example by Fst which makes the "Nilo-Saharan/East African" cluster in Somalis & Habeshas seem very "close" to the "Niger-Congo/West-Central African" cluster in Yorubas.
    Last edited by Awale; 02-02-2016 at 07:15 PM.

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    Quote Originally Posted by Khuur View Post
    From reading various posts by more knowledgeable and expert members in this forum, it seem that there are three big different groups genetically: West Eurasian, Sub-Saharan African and East Eurasian. Sometimes I also heard of this group term as South Eurasian in some posts as well.

    Megalophias put it really well, I'd say:

     
    Quote Originally Posted by Megalophias
    Sub-Saharan African isn't really a group, in fact you could divide all humanity into three groups of San, Pygmies, and Everyone Else if you wanted.

    Since humans have mixed repeatedly at different times and places, there isn't any particular number of groups that it makes sense to divide people into, it really depends what you are trying to achieve.


    There aren't always very rigid groupings particularly among various modern macro-populations and it depends on what you're trying to achieve. A lot of modern groups have over-lapping pre-historic ancestries from just around the last 5,000 to 25,000 years or so thus you can't rigidly divide them into these perfect branches. Nama (European and Horn African admixed), Maasais (Horn African and thus partially Near Eastern/West Eurasian), Europeans (draw ancestry from the Near East via CHGs and Anatolian Neolithic Farmers), South Asians (draw ancestry from the Near East through various sources like CHG-related ancestry and later Steppe ancestry) and East-Central Asians (are part West Eurasian with some of that ancestry ultimately being from the Near East) into these "four-branches" who descend from one node and then just differentiated from that point of origin like this:



    That's because many modern populations just like the Maasai, Nama and co. are mixtures of populations that existed before and many modern groups can over-lap in the pre-historic groups they draw ancestry from in just the last 5,000 to 20,000 years for example. You can definitely separate them because they are all very divergent via the ancestries they don't more recently share (the "Khoisan" in the Nama which isn't present in the Eurasian groups for example) and drift and they will cluster apart in PCAs but yeah... They're not exactly these perfectly separate branches of a tree.

    To conclude:

     
    "Real groups" might make more sense if we're dealing with ancients who are old enough not to be mixtures the way many of we modern folk are and for certain modern groups like un-admixed Khoisans Vs. Yorubas or Khoisans Vs. everyone else or un-admixed "African pygmies" (like the Mbuti) Vs. everyone else or East Asians Vs. Europeans but yeah. Even then... Where does the sub-grouping stop? You can start picking apart the "East Asian" grouping to differentiate the Japanese from Northeast Han thanks to the indigenous Japanese admixture in the Japanese or differentiate various West-Central Africans from each other even if something like ADMIXTURE is telling you that they're made up of the same cluster. And this is where Megalophias' comment about "what you want to achieve" comes in regards to grouping people. It's a messy business you want a straight answer for here, Khuur.

    If we go by what we've so far learned via both modern and ancient DNA there are a lot of apparent "core" ancestral nodes/cut-offs being noticed and conceptualized like European HGs + "ANEs" cutting off from what are for now classified as "Eastern Non-Africans" (which for now includes Austro-Aborigines, Papuans, East Asians and co. in the eyes of Iosif Lazaridis and David Reich for example) and then there's the theoretical "Crown Eurasian" cut off from a shared node with "Basal Eurasian" and then a cut off by the non-Neanderthal or Denisovan ancestors of all Eurasians from some sort of shared node with much of the ancestry in groups like Dinkas, Yorubas and so on and before a cut off with whatever shared node there is between everyone else and the likes of African Pygmies and the Khoisan. And honestly we need some ancient DNA to grasp Africa's genetic history better.

    So you're asking for straight answers for something we haven't fully figured out if we're discussing the core groups we're all descended from as the basis for "genetic groups". Granted, a lot of us in the modern era now are mixtures of these ancient groups rather than their uninterrupted descendants so you can't really group modern Europeans with East Asians the way you would group European Hunter-Gatherers with East Asians because of the Basal Eurasian ancestry in modern Europeans.


    Quote Originally Posted by Awale View Post
    But I'd sooner group Yorubas in a "node" with Eurasians to the exclusion of the Khoisan than the other way around. For various African populations, Fst, which measures differences in allele frequencies, is not as useful for measuring divergence as it is for Eurasian / Out-of-Africa populations who've suffered through lower population sizes (or dips like the "Eurasian bottle-neck") in early Human pre-history which were more conducive to genetic drift. For the African groups Haplotypic differences and stuff like dating on Haplogroups is more relevant and in that case you will notice some pretty hefty divergences like the African element in Somalis looking like it's separated from Yorubas by about ~40,000 years. This is contradicted for example by Fst which makes the "Nilo-Saharan/East African" cluster in Somalis & Habeshas seem very "close" to the "Niger-Congo/West-Central African" cluster in Yorubas.
    A lot of this occurred to the Sheikh very recently btw... I was having a conversation via email with a friend and we were discussing Omotic speakers in the Horn like Ari Blacksmiths and I just wasn't seeing his point about them being very divergent from East African Nilo-Saharan speakers like the Dinka or Anuaks because I was going off of Fst, IBS & ADMIXTURE then he explained to me how some of these methods can be misleading for various African populations and shared that study on the Khoisan. Found it funny that practically a few hours later this study came out and was going on about the same stuff he pointed out to me.
    Last edited by Awale; 02-03-2016 at 01:02 AM.

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    Guys there are plenty of other threads to talk about ancestral components and what they mean. This thread was started by someone with a specific question about Melanesian ancestry and where that fits in. If you want to discuss hypothetical components irrelevant to the OP, please start your own thread or carry on in one of the many similar threads in the Autosomal subforum.
     

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    Quote Originally Posted by Chad Rohlfsen View Post
    There three big families. Sub-Saharans, West Eurasians, and East Eurasians. Sub-Saharans are pretty complex and will probably take ancient DNA to figure out. Basically, it looks like the Khoisan are the first to split, followed by Mbuti/Bantu related, and then Yoruba/West Africans. There could be an East African group, but that is hard to tell for now. We may not have that pure group yet. Mota is West Eurasian admixed and appears to be a mix of Khoisan and West African. That is another story, and not really worth delving into very much. East Eurasians have a few branches, just as West Eurasians do. The Onge appear to own their own branch, along with another that is related to part of the Mamanwa and Papuans. The other branch is closely related to Han and Koreans. ASI is a sister branch to the Onge. The Onge branch also likely makes up over 50% of the ancestry of Papuans and Australians. Papuans and Australians form their own component due to Denisovan admixture, and also when an Onge and Ami/Atayal-based components are lacking. West Eurasians have two basic groups, EHG/MA1 and WHG. That is what we have, for now. Native Americans are a mix of West and East Eurasian. Ancient DNA will probably change what these components mean, as time goes on. We also have a component called Basal Eurasian. This is a branch off of the OoA group, about 80k years ago. This component is found in those with Near Eastern ancestry rooted somewhere between the UP and Mesolithic, and spread with the Neolithic. This includes modern Africans, Europeans, Central, South Central, and South Asians.
    What type of West Eurasian ancestry do most Native Americans (from North to South) have? Is it mostly in the form of ANE or EHG? Pardon me as I am still very new beginner to genetics. And what is the ratio East and West Eurasian are most Natives in terms of percentage?

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    Quote Originally Posted by Khuur View Post
    What type of West Eurasian ancestry do most Native Americans (from North to South) have? Is it mostly in the form of ANE or EHG? Pardon me as I am still very new beginner to genetics. And what is the ratio East and West Eurasian are most Natives in terms of percentage?
    This really depends on individuals. There's pretty well no Native Americans who don't have some European ancestry by now, so it's not particularly informative to analyze them using only three population groups, but the proportion of European ancestry tends to decrease as one moves away from the earliest-founded European population centres.

    The calculators with 9, 10, 11, and 13 components usually have Amerindian components but also a Siberian component (fairly common at low amounts in many Europeans but certainly not high there). One will also find both components at considerably higher proportions among Amerindians. These calculators usually have an Australasian component as well.

    In the Dodecad 10 spreadsheet, for example, you can see that Papuans register no Amerindian and are 100% Australasian, while Melanesians are 77.7% with zero Amerindian.

    No Native American groups appear to have any substantial Australasian -- in fact Europeans usually have more -- but you will find slight levels of the component in far South Asia and in Southeast Asia.

    So the short answer to your question is that if you were dividing the world into four groups, South Pacific people probably would not be one of them and would fit into the same category as Native Americans and East Asians; but with 9 or 10 groups and possibly fewer, certainly yes, with the proviso that there will be be quite some variety in this region and Hawaiians for example might end up closer to East Asia than to Papuans.

    I hope that helps.
     

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    Quote Originally Posted by AJL View Post
    This really depends on individuals. There's pretty well no Native Americans who don't have some European ancestry by now, so it's not particularly informative to analyze them using only three population groups, but the proportion of European ancestry tends to decrease as one moves away from the earliest-founded European population centres.

    The calculators with 9, 10, 11, and 13 components usually have Amerindian components but also a Siberian component (fairly common at low amounts in many Europeans but certainly not high there). One will also find both components at considerably higher proportions among Amerindians. These calculators usually have an Australasian component as well.

    In the Dodecad 10 spreadsheet, for example, you can see that Papuans register no Amerindian and are 100% Australasian, while Melanesians are 77.7% with zero Amerindian.

    No Native American groups appear to have any substantial Australasian -- in fact Europeans usually have more -- but you will find slight levels of the component in far South Asia and in Southeast Asia.

    So the short answer to your question is that if you were dividing the world into four groups, South Pacific people probably would not be one of them and would fit into the same category as Native Americans and East Asians; but with 9 or 10 groups and possibly fewer, certainly yes, with the proviso that there will be be quite some variety in this region and Hawaiians for example might end up closer to East Asia than to Papuans.

    I hope that helps.
    Thank you very much for explaining this to me! But I wonder is ANE a West Eurasian component? Karitiana score around 42% ANE based on in this West Eurasia K8: https://docs.google.com/spreadsheets...gid=1681484272 or ANE estimate if you go to #16: http://www.anthrogenica.com/showthre...alasians/page2.

    In this case does this mean Karitiana are around 41-42% West Eurasian? Can we say that Native Americans/Amerindians are a mixture of East+West Eurasian population?

    Thank you very much for your time!
    Last edited by Tsakhur; 04-08-2016 at 12:49 AM.

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    Quote Originally Posted by Khuur View Post
    I wonder is ANE a West Eurasian component? Karitiana score around 42% ANE based on in this West Eurasia K8: https://docs.google.com/spreadsheets...gid=1681484272 or ANE estimate if you go to #16: http://www.anthrogenica.com/showthre...alasians/page2.

    In this case does this mean Karitiana are around 41-42% West Eurasian? Can we say that Native Americans/Amerindians are a mixture of East+West Eurasian population?

    Thank you very much for your time!
    You're most welcome. I wouldn't know about exact ratios but at this point it's safe to say all Indigenous Americans have had some West Eurasian admixture from colonialism, which makes things harder to decipher. However, Karitiana people should be among the least-affected of Indigenous groups among the samples.

    The ancestral groups of Indigenous peoples appear to be mainly from Northeast Asia, which should correspond well with ANE, but with some evidence of West Eurasians in the founding populations. Witness mtDNA haplogroup X, which is found at highest frequency around the Near East and is spread thinly throughout Eurasia, even as far west as Ireland, but which also appears at high frequency, mainly in Algonquian speakers, in northeastern North America. So we have in effect at least two ancient waves or groups populating the Americas (disregarding the Inuit, who represent a distinct wave). I believe archeologists and linguists mostly support this view as well.
     

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    Quote Originally Posted by AJL View Post
    You're most welcome. I wouldn't know about exact ratios but at this point it's safe to say all Indigenous Americans have had some West Eurasian admixture from colonialism, which makes things harder to decipher. However, Karitiana people should be among the least-affected of Indigenous groups among the samples.

    The ancestral groups of Indigenous peoples appear to be mainly from Northeast Asia, which should correspond well with ANE, but with some evidence of West Eurasians in the founding populations. Witness mtDNA haplogroup X, which is found at highest frequency around the Near East and is spread thinly throughout Eurasia, even as far west as Ireland, but which also appears at high frequency, mainly in Algonquian speakers, in northeastern North America. So we have in effect at least two ancient waves or groups populating the Americas (disregarding the Inuit, who represent a distinct wave). I believe archeologists and linguists mostly support this view as well.
    Hmm you are right. Indeed, Indigenous Americans/Amerindians have some West Eurasian admix from recent colonialism. I learn from several members here that ANE is a West Eurasian or West Eurasian-related component. If one of the least affected groups by colonialism like Karitianas have ANE and ANE is really West Eurasian, I think it is possible to imply that there is another layer of West Eurasian-ancestry/affinity in Indigenous Americans that come even earlier than the period of colonialism if ANE is indeed West Eurasian/West Eurasian-related. This is what I think although it might be wrong as I learn more about the topic on this forum.
    Last edited by Tsakhur; 04-08-2016 at 03:26 AM.

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    Quote Originally Posted by Khuur View Post
    If one of the least affected groups by colonialism like Karitianas have ANE and ANE is really West Eurasian, I think it is possible to imply that there is another layer of West Eurasian-ancestry/affinity in Indigenous Americans that come even earlier than the period of colonialism if ANE is indeed West Eurasian/West Eurasian-related. This is what I think although it might be wrong as I learn more about the topic on this forum.
    I suspect you're quite right: there was almost certainly some West Eurasian–like genetics in the Americas before Columbus. On the other hand, I am not sure I would call ANE necessarily West Eurasian, it may have come from around the area that we now think of as the boundary between West and East: perhaps somewhere between where mtDNA X and yDNA Q spread from.
     

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    Quote Originally Posted by Khuur View Post
    Thank you very much for explaining this to me! But I wonder is ANE a West Eurasian component? Karitiana score around 42% ANE based on in this West Eurasia K8: https://docs.google.com/spreadsheets...gid=1681484272 or ANE estimate if you go to #16: http://www.anthrogenica.com/showthre...alasians/page2.

    In this case does this mean Karitiana are around 41-42% West Eurasian? Can we say that Native Americans/Amerindians are a mixture of East+West Eurasian population?

    Thank you very much for your time!
    There's isn't an exact definition of West Eurasian. Eurasian diversity doesn't fit a simple tree. MA1 is very related to WHG and his people contributed ancestry to at least some West Eurasians(for sure: Europeans and Caucasians), so in that sense MA1 was West Eurasian. He belonged to the same big extended and diverse family, that Upper Paleolithic and Mesolithic West Eurasians belonged to. MA1-related ancestry in Native Americans can be best explained as Western Eurasian, but it is only distantly related to any modern West Eurasians.

    You can just tell by Native Americans looks, there's no way 40% of their ancestry is from people who look anything like anyone in Europe or Middle East. If anything, MA1-like ancestry, represents the Dark skinned ancestors of Native Americans. Native Americans to me look like a mix of a people with generic-human or "Caucasoid" features and East Asians. Some look Eastern Asian in the face, and some don't, that's probably because of their ANE ancestry.

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