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Thread: The Puzzle of West Eurasian and SSA relationship

  1. #1
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    The Puzzle of West Eurasian and SSA relationship

    -In some ADMIXTURE runs, Natufians show SSA, Iran_N sometimes show SSA .. formal statistics show no evidence of SSA geneflow to Natufians.

    https://i.imgur.com/pA1R6kO.jpg
    https://static-content.springer.com/...MOESM1_ESM.pdf // Supplementary figure 4
    in a K=3 based calculator (Gedrosia K3 for example)

    -nMonte reduces SSA ancestry proportion when Natufians are used in a model, a component centered on Natufians in ADMIXTURE doesn't require SSA ancestry in some Near Easterners.

    https://anthrogenica.com/showthread....l=1#post336066
    https://media.nature.com/original/na...ms15694-s6.pdf // ADMIXTURE

    -TreeMix .. shows Natufians and Levant_N with some SSA geneflow .. formal stats show no evidence

    https://eurogenes.blogspot.com/2016/...an-puzzle.html

    -Fst between (SSA, West Eurasian) is less than (SSA, Eastern non-Africans), all West Euraisians, not just Near Easteners, North Africans, and South Europeans.
    -Fst between West Eurasian components and SSA components is less than Eastern components and SSA

    Pairwise FST values among 1000 Genomes Project and GME populations.svg
    https://anthrogenica.com/showthread....l=1#post408516

    -when estimating SSA ancestry proportion in modern and Ancient Egyptians in (Scheuenemann et al), the model is (WestEurasian + SSA), choice of WestEurasian changes the ancestry proportion of SSA, when it is ancient or modern near easterner, it requires less SSA, when it is ancient or modern European, it requires more SSA, the ancients are more extreme in their polarity, lowest SSA is with Iran_N and CHG, highest SSA is with MA1.

    https://media.nature.com/original/na...ms15694-s6.pdf // pages 10 and 11, qpAdm and f4-ratio

    -is there West Eurasian geneflow to SSA ? https://www.biorxiv.org/content/bior...62566.full.pdf
    or not ? https://twitter.com/iosif_lazaridis/...32000964726784

    -Haplogroup E is most likely African, given that old and diverse lineages are African.

    -reminder .. no evidence of SSA geneflow to Natufians.

    https://www.biorxiv.org/content/bior...59311.full.pdf // extended data table 1

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    It's no puzzle. There was ancient and prehistoric migration from Africa to Eurasia. Professional geneticists and amateur genetic bloggers find it too painful to accept.
    Last edited by Mansamusa; 08-07-2018 at 02:08 AM.

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    Quote Originally Posted by Mansamusa View Post
    It's no puzzle. There was ancient and prehistoric migration from Africa to Eurasia. Modern geneticists and amateurs genetic bloggers find it too painful to accept.
    but .. there is no evidence of any additional allele sharing between Natufians and SSA groups (Yoruba, Mbuti, Ju-Huan, Mota) other than the amount WHG, EHG, or SHG share, which is null .. check it, it's the last link.

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    Quote Originally Posted by IronHorse View Post
    but .. there is no evidence of any additional allele sharing between Natufians and SSA groups (Yoruba, Mbuti, Ju-Huan, Mota) other than the amount WHG, EHG, or SHG share, which is null .. check it, it's the last link.
    More than 90% of ancient DNA samples are European. We have close to no idea what the genetic profile of prehistoric or ancient SSA is. Yoruba, Mbuti, Ju-Huan, and even Mota, even if it's an ancient sample should not be assumed to represent ancient SSA or African genetic complexity.

    A wider range of Ancient SSA dna as old as or older than Natufians alone can settle the issue. Amateur genetic bloggers should stop taking advantage of the absence of ancient DNA samples from Africa to dismiss what is becoming increasingly obvious. In other words, you guys need to stop playing dumb.
    Last edited by Mansamusa; 08-07-2018 at 02:10 AM.

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    I'll tackle a few of these:

    Quote Originally Posted by IronHorse View Post
    -In some ADMIXTURE runs, Natufians show SSA, Iran_N sometimes show SSA .. formal statistics show no evidence of SSA geneflow to Natufians.

    https://i.imgur.com/pA1R6kO.jpg
    https://static-content.springer.com/...MOESM1_ESM.pdf // Supplementary figure 4
    in a K=3 based calculator (Gedrosia K3 for example)
    Taking presence of Africa+East Asian clusters in West Eurasians at K=2, as showing African admixture, is a lot like taking only PC1 from a Global PCA, seeing that West Eurasians would be closer to Africans (or East Asians, depending on the PCA input), then immediately concluding that they are admixed.

    It's just the case that in K=2 you effectively have reduced all genetic variation down to a single dimension (what would be one dimension in a PCA), and this has very low value as a summary of real variation.

    Even K=3 is probably no good for samples well outside of the range of present day variation, for the same reason as trying to project those samples onto a 2D PCA.

    Quote Originally Posted by IronHorse View Post
    -TreeMix .. shows Natufians and Levant_N with some SSA geneflow .. formal stats show no evidence

    https://eurogenes.blogspot.com/2016/...an-puzzle.html
    In most of those scenarios you see an edge from the base of the Eurasian tree, accounting for extra Basal Eurasian in Natufians. In those that you don't the edges are from a point either on the base of Mota's divergence with Eurasians - virtually Basal Eurasian - and in one instance very deep within the African clade between Mbuti and Yoruba - which is actually a deeper split viewed phylogenetically Eurasians and any extant Africa group!

    So those models show that in some specifications, Natufians can take ancestry from very deeply diverged positions in the human tree, at points where the most basal divergences of our species occur, in Africa (where e.g. Khoi branch from more northerly SSA before Eurasians branch from those more northerly SSA). That *could* represent some real ghost populations from south of the Sahara (though Green Saharan or north of the Sahara seems like a better guess to me, presuming this represents anything real at all), and if so they'd most likely have had a similar adaptation to climate, etc as most other SSA peoples.

    But they do not show any model where Natufians had any ancestry from any population that was evolving in a population clade with any extant known SSA populations, probably more recently than the Out of Africa event 70kya...

    Quote Originally Posted by IronHorse View Post
    -Fst between (SSA, West Eurasian) is less than (SSA, Eastern non-Africans), all West Euraisians, not just Near Easteners, North Africans, and South Europeans.
    -Fst between West Eurasian components and SSA components is less than Eastern components and SSA

    Pairwise FST values among 1000 Genomes Project and GME populations.svg
    https://anthrogenica.com/showthread....l=1#post408516
    Ancient dna tends to show that there are tons of West Eurasian ancient populations with higher Fst from African population than present East Asians - WHG, EHG, the Sunghir people, even the Natufians themselves (and though North Africa, not West Eurasia, then ancient Upper Paleolithic North African samples also).

    As you pool the genetic diversity of different populations, you find that they become closer to an outgroup, as measured by Fst, than any of the pooled populations are separately, or the average of any of the pooled populations. Uyghurs from Central Asia have lower Fst from West Africans than any European population, southern or northern, for this reason (as do many South Asian populations with no recent African ancestry), and Tatars who are Eastern European with a minority Siberian component have lower Fst from Africans than Eastern Europeans, even though Siberians have higher Fst from Africans.

    (Even in a modern context, think about why East Asians are probably not shown to be admixed with Africans by lower Fst from Africans than people from Papua New Guinea).

    West Eurasia had probably preserved more diverse streams than East Eurasia, going back through history to the Out of Africa even, so this kind of pooling effect will be more pronounced there (as I see it 90% likely, though there may be some issues of genetic ascertainment being biased towards West Eurasian diversity still, before this can be said to be 100% likely, and more whole genomes will deal with this).

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    Quote Originally Posted by Mansamusa View Post
    Amateur genetic bloggers should stop taking advantage of the absence of ancient DNA samples from Africa to dismiss what is becoming increasingly obvious. In other words, you guys need to stop playing dumb.
    They playing dumb....and will continue to do so. Just like Afrocentric loons be playing dumb acting like J1/J2, T1, or R1b carrying African populations were not affected by ancient Eurasian admixture. Its quite obvious there are going to be African genetic components that span multiple continents similar to ANE. Its also obvious that the African continent (East/South/West/North) is going to have some substructure that originated on the continent and spread outside of it probably signified by an extremely obvious Haplogroup E spillover.

    What is happening now is we are coming to the absurd conclusion that these Eurasian populations dont have African Admixture because 80kya......before crown Eurasians existed, certain genetic substructure on the African continent was not actually "African"..

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    This really confuses me:



    This was interpreted as evidence of gene flow between West Eurasia and Sub-Saharan Africa, fair enough, but then:





    So even Han and Onge show a negative signal, why wasn't it detected with Oceanians ? maybe it's because they have additional Archaic admixture ?
    Last edited by IronHorse; 08-07-2018 at 04:20 PM.

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    @IronHorse, Oceanians might show a negative score on the f4(Ust'Ishim,X;Yoruba,Chimp) stat, we don't know, as Lazaridis didn't include them in his panel.

    The stat involving Oceanians in the paper is f4(Ust'Ishim,X;Oceanian,Chimp), and shows that recent West Eurasians aren't (phylogenetically) closer to Oceanians relative to what Ust Ishim is. This is in contrast to the f4(Ust'Ishim,X;African,Chimp) stats where recent West Eurasians are closer to Africans than Ust Ishim.

    What Lazaridis's stats show is that the pattern of recent individuals being closer to Africans than Ust Ishim doesn't just apply to West Eurasia but also to East Eurasia. That makes it harder to explain the paper's idea that this pattern relates to West Eurasia->Africa gene flow (and this confounds only in West Eurasia the "indirect" Neanderthal estimate previously used).

    Visually, using Lazaridis's stats (as far as I can read them off) graphed against time:1uVaE3q.png. Shows change in the stat against time for both East and West Eurasia.

    Other stats from Lazaridis's twitter graphed against some other things:

    Direct Estimate of Neanderthal ancestry against sample time: cNp5Dud.png
    Direct Estimate of Neanderthal ancestry against Basal Eurasian estimate from Lazaridis 2016: OcEBA33.png
    Ust Ishim stat against Direct Estimate of Neanderthal ancestry: Xq8w1fQ.png

    Seems like the Ust Ishim stat is connected with sample time but not much with direct Neanderthal ancestry estimate, while the the direct Neanderthal estimate is connected with the Basal Eurasian estimate from Lazaridis 2016 (and the regression estimates 100% Basal Eurasian under this estimate would be lacking Neanderthal ancestry), but not otherwise with time (e.g. comparing the more recent European mesolithic HG to Upper Paleolithic HG, the direct Neanderthal estimate is as high or higher, even though they are later and have a higher shift towards Yoruba against the chimp outgroup compared to Ust Ishim). Obviously not much crossover in any of these sets, and more stats would work things out better.

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    Here is something to ponder:
    Not too long ago......Geneticists and amateur bloggers were arguing that Ancient North Africans would not have Any Sub Saharan (or even African) ancestry (12kya back migrant theory). After the publication of IAM amateur bloggers were still arguing that the Ancient North African Samples had no Sub Saharan Africa Ancestry. Then came the Taf samples. There are multiple lines of evidence that Eurasia have post OOA African gene flow....we just dont have the ancient African samples to resolve the specifics.

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    Quote Originally Posted by beyoku View Post
    Here is something to ponder:
    Not too long ago......Geneticists and amateur bloggers were arguing that Ancient North Africans would not have Any Sub Saharan (or even African) ancestry (12kya back migrant theory). After the publication of IAM amateur bloggers were still arguing that the Ancient North African Samples had no Sub Saharan Africa Ancestry. Then came the Taf samples. There are multiple lines of evidence that Eurasia have post OOA African gene flow....we just dont have the ancient African samples to resolve the specifics.
    Dude that's enormously wrong. What have back migration of eurasians in africa have to do with north africans and sub-saharian africans being related. Early European share similar genetic markers with modern Yoruba, San markers wich means that those 30'000 - 40'000 years old early europeans had close affinity with a common ancestor of modern african. No genetician or even serious blogger ever argue about this. You seem to think that having 1% of sub-saharians dna should do something morally to humans or i dont really where you want to go. You need to understand the following. Just make a little scenario, in 30'000BC a little group of Africans with a subclade of haplogroup E goes to Arabian Peninsula / Middle-East and stays here for like 20'000 years. 10'000 BC if those same people didn't have constant african gene flow, but had eurasian gene flow, they would lost probably most of their ancestral african markers. Genotype and Phenotype are too different things. You can look very european with all physical characteristics and have 10% of sub-saharian dna, what's the point you want to prove? What have hypothetic ancient african ancestors for an european would implying to you?

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