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

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    Quote Originally Posted by Ramses View Post
    Taforalt in PCA doesn't act like a 45% african 55% eurasian population , they act like a 65% Eurasian just like they get in other admixture runs and calculators.

    In PCA they are more Eurasian shifted than Ethiopean Jews and Early Pastoral kenya who are about 55% Eurasian.

    Also Natufians don't act like a population with 13% african ancestry which is the ANA percentage in them according to the Dzudzuana paper , modern egyptians who show similar african percentage are more african shifted than natufians.



    So PCA is more aligning with there Admixture, or that ANA is not a simple african ancestry but an ancestry that does share some Eurasian tendencies maybe due to its phylogenetic position.
    I also want to mention that some recent papers didn't even take ANA into consideration and just continued treating Taforalt as 65% eurasian , 35% african.

    Don't you think its a little bit intellectually dishonest to use the Natufians for your nmonte model when we know full well that the Natufians have Iberomaurusian like ancestry which is absorbing some of the African affinity in the Iberomaurusians. Try running the same model with Barcin and you will definitely see that the 45-55 split is pretty robust.

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    Quote Originally Posted by Mnemonics View Post
    Don't you think its a little bit intellectually dishonest to use the Natufians for your nmonte model when we know full well that the Natufians have Iberomaurusian like ancestry which is absorbing some of the African affinity in the Iberomaurusians. Try running the same model with Barcin and you will definitely see that the 45-55 split is pretty robust.
    Out of curiosity, how much IBM do modern North Africans have using qpAdm?

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    There are very slight variations in Dzudzuana:ANA ratios among Taforalt individuals.

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    Quote Originally Posted by JRD View Post
    There are very slight variations in Dzudzuana:ANA ratios among Taforalt individuals.
    The fun part of this is, Dzudzuana is real, Basal Eurasian and ANA is not. They are just modelled ghosts. So we might see something close to reality, but talking about slight variations in such models might be just too much. The real samples might change a lot.

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    Quote Originally Posted by Riverman


    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 fat 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 one aspect, but forgetting about the second: You get closer to another population on the PCA, if you share ancestry.

    So the real question is, were 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.
    To be fair, I wouldn't be too distracted by the ANA simulation by Korotyr itself in those PCAs. I just threw it in there for the heck of it. The pull toward "SSAs" that IBMs show is clear enough on its own. Even if Ramses was right, which he is clearly not, he doesn't really seem to get that what he says doesn't disprove anything and he was basically arguing semantics like the exact ancestry proportions and not getting to crux of the issue. Whether 20 or 60% Non-Eurasian they still clearly pull away from Eurasian bottleneck groups the way an admixed Eurasian:SSA group does and the position they pull away to weirdly aligns quite well with the Dzudzuana paper's estimation for ANA ancestry (~45%) in that when you use formal-stats and suss out the exact Eurasian scores of a group like Tigrinyas it is about 50% of their ancestry so being just a bit closer toward Eurasians in the plot than Tigrinyas like that fits alarmingly well. Top that off with the stats showing clear but unique SSA-related affinities (even toward Mbutis) and qpGraphs like the one in the study and it's pretty damning as to where ANA likely clustered on a global PCA.

    Quote Originally Posted by Riverman
    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.
    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. 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.

    Quote Originally Posted by Riverman
    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.
    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.

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    Quote Originally Posted by Awale View Post
    But thank you for finally pointing out to everyone on this forum that you really don't know what you're talking about or you would have known all this.
    Don't thank me I didn't show anything yet lol..

    mentioning formal stats , but ignoring what i just posted about PCA position of Taforalt as if there is any discrepancy , what does that has to do with Taforalt position in PCA?
    What did you intend by this meaningless comment ? on the other side formal stats also depends on the used West Eurasian source.
    second. I'm actually basing my comment on the original admixture Found in Taforalt in its original paper. Before i do base it on G25 calculator.

    Here's more "Official conclusions from the taforalt study
    They cluster in intermediate position between east africans and north africans , not with East africans..

    " When projected onto the top principal components of African and west Eurasian
    populations, the Taforalt individuals form a distinct cluster in an intermediate position between
    present-day North Africans [e.g., Amazighes
    (Berbers), Mozabites, and Saharawis] and East
    Africans (e.g., Afars, Oromos, and Somalis) (Fig. 2A)"
    And Yes Natufians still more Eurasian shifted than egyptains.


    ha , using "formal stats" from the original study they are 63.5% Natufian

    "We calculated outgroup f3 statistics of the form
    f3(Taforalt, X; Mbuti) across worldwide ancient
    and present-day test populations. Consistent with
    previous analyses, we find that ancient Near Eastern populations, especially Epipaleolithic Natufians
    and early Neolithic Levantines, show the highest

    We investigated whether two first-hand proxies,
    Natufians and West Africans, are sufficient to
    explain the Taforalt gene pool or whether a more
    complex admixture model is required. We thus
    tested whether Natufians could be a sufficient
    proxy for the Eurasian ancestry in Taforalt without explicit modeling of its African ancestry (fig.
    S18). ....A two-way
    admixture model, comprising Natufian and subSaharan African populations, does not significantly deviate from our data (c2 P ≥ 0.128), with
    63.5% Natufian and 36.5% sub-Saharan African

    ancestry, on average (table S8). Adding Paleolithic European lineages as a third source only
    marginally increased the model fit (c2 P = 0.019
    to 0.128; table S9). Consistently, by using the
    qpGraph package (21), we find that a mixture
    of Natufian and Yoruba reasonably fits the
    Taforalt gene pool (|z| ≤ 3.7; fig. S19 and table S10)"

    Although the oldest Iberomaurusian microlithic bladelet technologies are found earlier
    in the Maghreb than their equivalents in northeastern Africa (Cyrenaica) and the earliest Natufian in the Levant, the complex sub-Saharan
    ancestry in Taforalt makes our individuals an
    unlikely proxy for the ancestral population of
    later Natufians who do not harbor sub-Saharan
    ancestry
    Admixture graph showing no african ancestry in Natufians and showing Natufians giving about 63%-70% to Taforalt.


    Again No Sub-saharan ancestry found in Natufians from Lazaradis 2016 using "formal stats"

    "However, no affinity of Natufians to sub-Saharan Africans is evident in our genome-wide analysis, as present-day sub-Saharan Africans do not share more alleles with Natufians than with other ancient Eurasians"





    Quote Originally Posted by Mnemonics View Post
    Don't you think its a little bit intellectually dishonest to use the Natufians for your nmonte model when we know full well that the Natufians have Iberomaurusian like ancestry which is absorbing some of the African affinity in the Iberomaurusians. Try running the same model with Barcin and you will definitely see that the 45-55 split is pretty robust.
    "Natufians have Iberomaurusian" is just a model , a hypothesis..it doesn't mean Natufians really have Iberomaurusian..
    This G25 run was based on the inferred Natufian admixture in Taforalt previously known which has almost similar percentage. Also Natufians don't have sub-saharan ancestry it can't absorb something it doesn't have...ANA on the other hand is just another model.
    Natufians can also be modelled as mixture of BE and CWE , from which it serve easily as Eurasian source to Taforalt.

    lastly , Anatolia Barcin are not the best source to be used to Taforalt first because they are not an ancestor to them.., second because of there lower Basal Eurasian ancestry which will hinder part of the Deep ancestry used on the tested population. The same way it does with IranN.
    Last edited by Ramses; 11-30-2020 at 11:12 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?
    If someone can answer this please

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    Mnemonics, if you don't mind one more request, does Morocco_EN (IAM) need additional Levantine input in order to be successfully modeled in qpAdm? Or do they basically just look like unadmixed IBM descendants?

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    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:

    1-s2.0-S1875176819301489-gr1.jpg

    On another note if the Shum Laka paper was the most recent to model IBM, and had them at ~47% 'SSA' what's the problem? Amateur geneticists do a better job?

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    Quote Originally Posted by Ramses View Post
    Don't thank me I didn't show anything yet lol..

    mentioning formal stats , but ignoring what i just posted about PCA position of Taforalt as if there is any discrepancy , what does that has to do with Taforalt position in PCA?
    What did you intend by this meaningless comment ? on the other side formal stats also depends on the used West Eurasian source.
    second. I'm actually basing my comment on the original admixture Found in Taforalt in its original paper. Before i do base it on G25 calculator.

    Here's more "Official conclusions from the taforalt study
    They cluster in intermediate position between east africans and north africans , not with East africans..


    And Yes Natufians still more Eurasian shifted than egyptains.


    ha , using "formal stats" from the original study they are 63.5% Natufian

    "We calculated outgroup f3 statistics of the form
    f3(Taforalt, X; Mbuti) across worldwide ancient
    and present-day test populations. Consistent with
    previous analyses, we find that ancient Near Eastern populations, especially Epipaleolithic Natufians
    and early Neolithic Levantines, show the highest

    We investigated whether two first-hand proxies,
    Natufians and West Africans, are sufficient to
    explain the Taforalt gene pool or whether a more
    complex admixture model is required. We thus
    tested whether Natufians could be a sufficient
    proxy for the Eurasian ancestry in Taforalt without explicit modeling of its African ancestry (fig.
    S18). ....A two-way
    admixture model, comprising Natufian and subSaharan African populations, does not significantly deviate from our data (c2 P ≥ 0.128), with
    63.5% Natufian and 36.5% sub-Saharan African

    ancestry, on average (table S8). Adding Paleolithic European lineages as a third source only
    marginally increased the model fit (c2 P = 0.019
    to 0.128; table S9). Consistently, by using the
    qpGraph package (21), we find that a mixture
    of Natufian and Yoruba reasonably fits the
    Taforalt gene pool (|z| ≤ 3.7; fig. S19 and table S10)"


    Admixture graph showing no african ancestry in Natufians and showing Natufians giving about 63%-70% to Taforalt.


    Again No Sub-saharan ancestry found in Natufians from Lazaradis 2016 using "formal stats"

    "However, no affinity of Natufians to sub-Saharan Africans is evident in our genome-wide analysis, as present-day sub-Saharan Africans do not share more alleles with Natufians than with other ancient Eurasians"






    "Natufians have Iberomaurusian" is just a model , a hypothesis..it doesn't mean Natufians really have Iberomaurusian..
    This G25 run was based on the inferred Natufian admixture in Taforalt previously known which has almost similar percentage. Also Natufians don't have sub-saharan ancestry it can't absorb something it doesn't have...ANA on the other hand is just another model.
    Natufians can also be modelled as mixture of BE and CWE , from which it serve easily as Eurasian source to Taforalt.

    lastly , Anatolia Barcin are not the best source to be used to Taforalt first because they are an ancestor to them.., second because of there lower Basal Eurasian ancestry which will hinder part of the Deep ancestry used on the tested population. The same way it does with IranN.
    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.

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