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Thread: The mixed genetic origin of the first farmers of Europe

  1. #251
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    Quote Originally Posted by Mnemonics View Post
    The Natufians definitely have real Iberomaurusian ancestry the formal stats very strongly support this. Try Pinarbasi if you are concerned about the tiny Levantine affinity in Barcin, although it is odd that you are concerned about one population being decended from another when you are perfectly willing to model Iberomaurusians with Natufian. The Natufians definitely have ANA and AEA affinities I can model them pretty plausibly with 6% Dinka/Mota and 15-14% Iberomaurusian which comes to about 12.5% African affinity.

    Now let's take that 63.5 percent Natufian and find the missing African affinity, and we get 7.95% African being absorbed by the Natufian add that to the 36.5% African and what do we get?
    44.4% African just like the formal stats consistently say.
    I can also model IranN with Barcin+Dinka , it doesn't has to be true admixture , its simply the excessive deep ancestry not accounted for.
    Natufians don't differ from other ancient Eurasians in there relation to Sub-saharan africans in there allele sharing . Which means they are as Eurasian as WHG.
    and Can be used as Eurasian source to Taforalt as per the pervious mentioned studies.

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    Quote Originally Posted by Riverman View Post




    I tell you why that kind of argument is problematic, its for two reasons:
    1. Its no real ANA and ANA is likely to have been quite diversified, which leads to the spread of "Neo-African" or "ANA-like" to the rest of Africa, but that much later. I saw various "ghost models" here and elsewhere, over the years. Some came close to the real thing, when it was retrieved, others were or are horribly wrong. Even by one look you see someone did a bad job. Now I'm not saying that for this ANA model, but I just want to caution against "taking it for the real thing", when it is not.

    2. If you put it on a PCA like that, people might say, "look, its closer to SSA", but there is a problem with that kind of interpretation. Because the closeness comes not just from ANA being close to modern SSA, but from the fact that modern SSA have ANA and ANA-like ancestry at a high proportion! So its close to arguing in favour of a closeness of let's say Egyptians and Yemenites to Ethio-Semites, which is real, only based on one aspect, but forgetting about the second: You get closer to another population on the PCA, if you share ancestry, regardless of the direction of the flow.
    So the real question is, where would Africans without that ANA-like/Neo-African ancestry be put on the PCA, and who would be closer then? I think we all know the answer, ANA would be closer to Eurasians. Even though modern SSA have a lot of ANA-like ancestry, they are still, just going by the model you used, which isn't the real thing, quite far apart.

    This means yes, ANA is not Eurasian proper, not Basal, not Main Eurasian, but its the closest neighbour by a margin from the African variation. And that's no coincidence.



    If there would have been this kind of deep multiregionalism, undistorted, they would be completely different people. The, like you said, Neo-African/ANA-like ancestry went over the continent in different waves and brought the populations closer together and closer to Eurasians, because this wave, its origin, was much closer Proto-Eurasians by default. So its important to change perspectives, exactly like I described for the PCA above. That ANA-like ancestry can be considered closer to SSA is because it constituted them, not because it was, originally, closer to Basal African H.s. That's a huge difference for the understanding. Because it implies that a related group to the Proto-Eurasians formed practically all of modern Africans, not "deep African ancestry" having flown into e.g. IBM.

    Once we get genomes of people before the "big back-migraton event" (Near East or North East Africa), the importance of the distinction will become apparent. Shum Laka was just some generations too late probably, Mota is probably the result of not just the first, but a second or third wave hitting East Africa. We're really dealing with more distant timings, because ANA-like ancestry is supposed to have spread minimum for 40.000 years in Africa when Mota was alive. That's obviously much too late for any kind of reference, especially since Eastern Africa was surely earlier hit by the expansion, than Western tropical Africa, the region where Shum Laka was found. So Mota is probably further away because it was an earlier branch of this Neo-Africans which moved down in the East and already mixed with locals as well.
    On the contrary, those found in the IBM were relatively "pure" and closer to the population's centre in North East Africa. With that perspective, all the events get turned around, if true. It makes clear what the centre vs. periphery dichotomy really was. Its absolutely ridiculous, like it was done with the South African finds, if some articles claimed that they found the cradle of humanity in South Africa and some authors even implied we all descend from a San-like people. First of all, the San are a modern H.s. group with its own evolutionary history and admixture events, they are no living fossil, secondly what is older about them, is because they came to be by an earlier branching event, in which they took more basal clades with them and preserved these in their fairly small and isolated population, until they made new contacts.

    The same will be seen with the non-Basal African ancestry in Mota: It was an earlier branching event creating it in comparison to the ANA-central groups in North Africa. The distance made them somewhat, not by a lot, more distant from Eurasians, together with the Basal admixture. The kind of arguments like this or that people descend from Mota, because they show similarities, is misleading, because it confuses source with target. The Mota HG were not source, but the target of gene flow. Like some hundreds of thousands of years earlier the ancestral San component was the target, not the source. Ultimately, the main source for most movements in recent Africa will be found to be either ANA-like (especially Niger-Kordofanian) or BEA-WEA (Afro-Asiatic). I think the connection is quite clear. And there were even earlier such expansions, among hunter gatherers, which being already lost under the newer layers and hard to recognise.
    If they can analyse older samples however, it will become evident.

    There can be no correct model or estimate without knowing the true baseline for a reference. And in the African context, we are very far from it. I mean in the African context we have something like Mota, which is for Europe like LBK. That's much too late.
    But Africans are in fact very "very different people", when people talk about genetic diversity in Africans they're not joking!

    Nobody disagrees with you on your last point, of course many African populations will be closer to Eurasians than to African HGs, by that standard even Yoruba can be considered "Eurasian". I just think you greatly overexaggerate the importance of groups closely related to Eurasians in creating "Neo-Africans", and that there's little credence in the idea that they are descended mostly from an tightly interrelated group within which Eurasians arose, or that this maybe has something to do with changes in the African archaeological record even (with your claims about "centre-periphery relations"). For the archaeology this is just incorrect--there's a lot of evidence for complex behaviors flickering on and off throughout Africa starting from the MSA; for the population genetics people who have dated population splits even within the "Neo-African" group (e.g. Schlebusch et al) get extremely old times (e.g. ~135kya for Yoruba-Dinka split), indicating that "Neo-Africans" are deeply rooted in Africa within the deep substructure there. Despite its clading together with Eurasians to the exclusion of Basal human HGs, the bulk of ancestry of "Neo-Africans" is not that closely related to each other.
    Last edited by Ryukendo; 12-01-2020 at 12:10 AM.
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    Quote Originally Posted by Awale View Post
    Whether 20 or 60% Non-Eurasian they still clearly pull away from Eurasian bottleneck groups the way an admixed Eurasian:SSA group does
    That's correct. In a way the ANA could be seen as intermediate, not strictly, probably better as an intermediary. Where exactly they will be plotted, unadmixed, is another issue. Because what we didn't talk about is another factor: If the Proto-ANA and Proto-Eurasians split, and dispersed, they weren't moving into no man's land. So the Proto-ANA might have been even closer to Eurasians, than the ancestral component detected later, because on their way West, just like the BEA-WEA component in IBM, they did mix, like they did mix in Mota too. Unless all of North Africa was one big ANA-homeground, which is debatable and the main reason I'm actually arguing. I don't think that this "Neo-African"-component was anywhere near as widespread 70.000 years ago.

    I think there are some issues with this assumption like South-African HGs. Correct me if I'm wrong but I have not seen any models showing the SAHG samples we have at all admixed in the direction of anything relating to ANA or seeming phylogenetically close to it like most of the ancestry in Mota.
    That's correct. But there are such ridiculous claims around which made Proto-San the ancestors of all of mankind and stuff like that, which is obviously even more absurd. I think not too many scientific groups will claim it unless its bulletproof. And as things stand, it can only become bulletproof, once we get old, really old, ancient DNA from Africa. But let's forget about that for a moment, let's just pretend that problem doesn't exist and SA-HG are really the unmixed pristine Africans, which I don't think they can be, but ok.

    Yet ancient SAHGs pretty much cluster to the other side of Eurasians like any other "SSA" group and in the same direction as we can assume ANA would based on the clustering of IBMs. So I think it still stands so far that the Eurasian bottleneck was quite a deep drift event and global PCAs notices that before finally seeing the deep structure in Africa.
    Sure, there was the Eurasian bottleneck on the one hand and African diversity being increased by a combination of backmigration plus intermixture between highly divergent ancestral, regional groups. Multiregionalism, like you said, masked by Eurasian outgroups on a global PCA. Even a fairly small amount of the more Basal Ancestry gives a strong global pull, think that is the takeaway.

    Sure. It seems phylogenetically closer to Eurasians than other components in Africa do. That's fairly clear. This is probably either due to most of the ancestry in it being a sister group to proto-Eurasians or early admixture from Eurasians or both.
    Exactly. And I want to find out or debate what it could have been. Which clues the current data might provide.

    Quote Originally Posted by ThaYamamoto View Post
    Not invested in any particular argument or stance so I ask this without any bias, how do we explain L3 lineages dominating west-Africa, even more so than I originally thought e.g. this recent study in Nigerian Yorubas which surprised me quite abit:

    Attachment 41476
    That's another important aspect of the story. West Africans descent to a large degree from ANA-like people moving into the region, crossing the tropical and Malaria borderline, probably helped out by admixture with locals, which gave the more mixed population the edge over "more pure" groups. Actually quite similar to the situation in South Asia, where both the incoming Iranian agro-pastoralists and the Indo-Aryans would have had, probably, a harder time, needing longer, to adapt to the region. This is an important biogeographical barrier. So the real question is, why did they get so much non-E and non-L3 derived lineages, still. And the answer might be just that, regional adaptation to cross the biogeographical borderline.

    Another question is how selection would change, once the biogeographical barrier was crossed. Like if one group had lactase persistence in Northern Europe, it got the edge initially, even in an unfavourable admixture event, they could still profit from that advantage. But on the long run, once the favourable allel being nearly fixed in all of the newly emerging mixed population, other factors might become more important. That's another thing we can't explore without older African DNA, how mixture events took place and which selective trends followed, or how these changed over time. Some can be reconstructed with highly sophisticated models, but we see it with lactase persistence in Europe again. Without the real data from the ancient DNA, a lot remains speculative and needs to be corrected once the data comes in. Like almost nobody had such a late date for the spread of lactase persistence in mind before the actual results from the ancient remains came in.

    And I guess we will get similar surprises for Africa, if we ever get the data...

    What the data shows, however, is how much of a replacement took place, not just on the paternal side (hg E), but also on the maternal (L3). And considering that the majority of their ancestors seem to have lived much further to the North before the Sahara dried up, that seems to have been quite a migration period. Like I said, big chain migration events were at work to form the modern populations. Go more than 10.000 years back in time and there were still Iwo Eleru like archaic Homo people hunting in the forests which were later cleared by Niger-Kordofanians.
    Question is how long did AMH live in the region, how long beside Iwo Eleru-like people and what was the exact profile of these Iwo Eleru people, did anything survive. Interestingly going by the same haplogroup evaluation, it doesn't look like too much did. But we also have no yDNA and mtDNA from Neandertals, yet their autosomal contribution is still there.

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  6. #254
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    Quote Originally Posted by Ramses View Post
    I can also model IranN with Barcin+Dinka , it doesn't has to be true admixture , its simply the excessive deep ancestry not accounted for.
    Natufians don't differ from other ancient Eurasians in there relation to Sub-saharan africans in there allele sharing . Which means they are as Eurasian as WHG.
    and Can be used as Eurasian source to Taforalt as per the pervious mentioned studies.
    I'm talking about a formal stats based model like qpadm.

    Direct F4stat comparisons are hard to do when we lack the populations involved in the admixture especially when we are talking about African and Eurasian admixture. It can get so weird that Somalis strongly prefer Eurasians over other Somalis.
    Last edited by Mnemonics; 12-01-2020 at 01:12 AM.

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    Quote Originally Posted by Keneki20 View Post
    Unfortunately, I don't think I can give you a satisfactory answer to your first and last questions right now. Although, as for Iberomaurusians samples so far yielding only E lineages (and the lack so far of native mtDNA lineages), I think that exogamy may be able to help explain that. Amongst the Ongota in Ethiopia, for example, Ongota men apparently tend to marry Ts'amakko women and not Ongota women. The same applies with respect to the neighboring Gawwada.
    These are some interesting examples of HG exogamy but I'm not sure I really buy them as possible mechanisms to explain the IBM E vs M1/U6 discordance. If Ongota men really did continuously marry Ts'amakko women, then after a couple generations the "Ongota" people would barely even be Ongota autosomally anymore, instead they would be overwhelming Ts'amakko both autosomally and in mtDNA with only Ongota y-DNA left basically.

    But this is not the case with IBM, they are apparently a nearly 50-50 blend of ANA-Eurasian. Which means a small cadre of E (ANA) men consistently adopting M1/U6 (Eurasian) partners doesn't make sense, because if that was the case then IBM would be overwhelming Eurasian and only a small minority ANA.

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    Quote Originally Posted by CopperAxe View Post
    PIE was spread by EHG lineages from the PC Steppe. R1a-m417 and r1b-m269 are examples of such lineages. But EHGs also had other haplogroups like I2, J and Q. Therefore those lineages could've been spread by the early Indo-Europeans as well.

    Q and R are related Y-dna haplogroups, and they are equally intrusive to Europe.

    Not sure why people here think that any Q in the west is via migrations from Altaic or Mongoloid peoples here, when it is clearly ANE related.
    Most probably because Q has branches that are either exclusive to certain areas in south/east Asia or they are completely absent in indo european communities like Q1b1.

    I guess it comes down to how successful Q linages were in europe. It barely exists in west eurasia while in south american natives, it makes up 90% of the linages.
     

    Target: Xeon_scaled
    Distance: 2.7735% / 0.02773461

    33.0 IRN_Ganj_Dareh_N
    20.6 Levant_PPNC
    18.4 TUR_Barcin_N
    14.4 GEO_CHG
    13.2 Yamnaya_RUS_Samara
    0.4 RUS_Devils_Gate_Cave_N

    Target: Xeon_scaled
    Distance: 2.2807% / 0.02280652

    37.0 Kura-Araxes_ARM_Kaps
    24.0 IRN_Ganj_Dareh_N
    17.4 Levant_PPNB
    11.2 Yamnaya_RUS_Samara
    4.4 Anatolia_Barcin_N
    4.0 Anatolia_Tepecik_Ciftlik_N
    1.4 Nganassan
    0.6 MAR_Taforalt

  11. #257
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    Quote Originally Posted by ThaYamamoto View Post
    Not invested in any particular argument or stance so I ask this without any bias, how do we explain L3 lineages dominating west-Africa, even more so than I originally thought e.g. this recent study in Nigerian Yorubas which surprised me quite abit:
    I read that a few months ago, and it indeed seems to verify a trend I've noticed in West African populations at large. That is, L3 lineages tend to be far more common than is publicized. Well, at least, they're more common than I initially imagined.

    In another study titled Little genetic differentiation as assessed by uniparental markers in the presence of substantial language variation in peoples of the Cross River region of Nigeria, L3 lineages in the Igbo were at 38.31%. If counting non-L lineages (unspecified) with L3, then that figure jumps to 39.3%. I had to calculate that from the supplementary notes, though, as the graphic it gives, while useful, isn't the easiest to parse out information from. In the same study, the L3 figure (at least from the graphic. I didn't calculate this particular figure myself) is higher when looking at Nigeria at large. For Ghana, the L3 figures were a little bit lower, but still very significant (at least in the 20s percentage-wise).

    Then, when seeing both Nigerians and other West Africans taking 23andme tests, their mtDNA results would show L3 lineages slightly more often than L2 or even L1 lineages, which were what I initially expected. A bit surprising, especially since L2a tends to be uniformly the most common distinct mtDNA lineage amongst West Africans.

    For the first study you mentioned, though, it may be a bit problematic. I remembered seeing it and adding up the figures it presented. I fell just short of 100% every time. That's to say, everything (L3b+L3d+L1c+L2c,+ etc.) added up to 97.26%, when it shouldn't have. Maybe that was due to rounding, since many haplogroups had the exact same frequencies too often to make sense. But still, the fact that I could never get 100% when adding all haplogroups up was a bit troubling. Anyway, when adding up L3 lineage frequencies it presented, the total figure was just 50.75%. As for L2 lineages, they were only 28.18%, which is relatively low and a bit odd to me. I suppose that just may be down to the individuals sampled.

    Although, a doctoral dissertation titled Tracing the genetic origin of African descendants from South America (also Origine génétique des descendants Africains de
    l’Amérique du Sud)
    , and one other study titled Contrasting Maternal and Paternal Histories in the Linguistic
    Context of Burkina Faso
    seem to suggest that L3 lineages are about as common as amongst the Yoruba as L2 lineages are. At the very least, their frequencies are comparable. In the dissertation, if tallying up the L3 and L2 lineage frequencies (page 131), the Yoruba (in Benin) had a 50.1% L3 frequency and a 37.5% L2 frequency. So, once again, another frequency in the range of 50%. For the other study, on the other hand, it said Yoruba's had a 41% L2a frequency and a 37% frequency of L3 lineages. That information is deduced from the supplementary notes. Actually, for this study, L2 is sometimes even consistently the most common in West Africans, but L3 is seldom ever far behind.

    Overall, with respect to your comments on the large presence of L3 in West Africans, it's significant presence is noteworthy.


    As for your inquiry on why L3 is so present, I can't offer all that much. However, I did find an interesting quote from one of an article titled Genetic diversity between two Igbo men from Owerri senatorial province as determined by autosomal short tandem repeats, Y-chromosomal short tandem repeats and mitochondrial DNA typing methods. Not sure exactly how meaningful the information it brings up is, but it's still interesting:

    The collective polymorphism profile of UMBACK haplotype indicated that his mtDNA haplogroup — a specific genetic population to which he belongs is L3e2b. This group is associated with mtDNA D-loop HVS-1 sequence motif (172-189-223-320). The L3e clade is the most widespread, frequent, and ancient of the African L3 clades, comprising approximately one-third of all L3 types in sub-Saharan Africa. [16]


    This haplogroup has recently been discussed in detail by Bandelt et al.[17] who suggested an origin for the haplogroup to be in the Central Africa/Sudan region ~45,000 years ago. The subclade L3e2b is found primarily in West Africa, This indicates a range expansion from Central into West Africa (~9,000 years ago). In contrast, ELAMBIA’s mtDNA haplotype belongs to L3f1b1 haplogroup. This group is associated with HVS-1 sequence motif (209-223-311). This haplogroup is also shared by West and South-East Africans.

    At the same time, several L3f types are shared uniquely by West Africans only. L3f is likely of East African origin according to Salas et al. [16] but the derived sub-haplogroup L3f1 is also present in West Africa, and it is this component that is most commonly found in Americans. It is thought that L3f1b1 lineage to which ELAMBIA belongs is dated to 9,200 years, while UMBACK L3e2b lineage arose earlier approximately 9,000 years.
    Last edited by Keneki20; 12-01-2020 at 02:11 PM.

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    Quote Originally Posted by TuaMan View Post
    Out of curiosity, how much IBM do modern North Africans have using qpAdm?
    Do you know what population best represents the Iberian admixture in North Africans?

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    Quote Originally Posted by Mnemonics View Post
    Do you know what population best represents the Iberian admixture in North Africans?
    Probably some other user here who's tinkered a lot with G25 would be better able to answer.

    Just going off of this paper:
    https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6042094/

    I think the Iberia_EN.SG sample in the 1240k dataset might be good enough, at least preliminarily?

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    Quote Originally Posted by Xeon View Post
    Most probably because Q has branches that are either exclusive to certain areas in south/east Asia or they are completely absent in indo european communities like Q1b1.

    I guess it comes down to how successful Q linages were in europe. It barely exists in west eurasia while in south american natives, it makes up 90% of the linages.
    Nobody said all Q is related to PIE. Some subclasses of Q1a though yes. There's also plenty of non IE R1b like M73 and and V88 and some old subclades of R1a as well.

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