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Thread: The puzzle of West Eurasian and SSA relationship

  1. #1
    Elite member IronSide's Avatar
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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

    https://commons.wikimedia.org/wiki/F...opulations.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

  2. #2
    Advisor Angela's Avatar
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    Quote Originally Posted by IronSide 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)
    -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
    https://commons.wikimedia.org/wiki/F...opulations.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
    The last thing I remember reading about this is that the paper finding West Eurasian gene flow into SSA was incorrect. It was actually only in East Africa and down to South Africa that it could be found.

    In terms of the Natufians, it has always seemed to me that they might have ancestry from, say, the area near modern day Egypt or the Red Sea which is separate from SSA, a different kind of African, if you will, for which we have no ancient samples. Groups with some proportion of that ancestry may have continued on into the southern Levant for quite some time.

    As for fst SSA closeness to West Eurasia AND East Eurasia, with SSA being closer to East Eurasian, I don't know. I haven't investigated it closely. Could it be related to differing amounts of really archaic ancestry?


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