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Thread: What pops should I used to gauge the percentage of West Eurasian in East Africans?

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    What pops should I used to gauge the percentage of West Eurasian in East Africans?

    Sorry for asking this but I am pretty much a novice in African population genetics. I know a lot more about the basics of SE Asian genetics as I from that region myself.

    I am eager to figure out the percentage of African vs West Eurasian genetic contributions/ancestries in East African populations. From my vague and layman understanding, the West Eurasian ancestry is East Africa is primarily Levant_Neolithic/SW Asian-related and the African ancestries are predominantly Nilotic, Cushitic, Bantu/Niger-Congo and some Omotic or Hadza-related stuff?

    I want to know what ancient pops should I used to determine the amount of West Eurasian and African genetic proportions in East Africans especially the non-Horner ones.

    Can anyone help or give me suggestions please?

    I want to compare and figure out who possessed more West Eurasian ancestries: non-Horner East Africans or SE Asians. SE Asians are predominantly Dai (Southern Chinese rice-farmer)/Taiwanese Aborigines+Negrito/Hoabinhnian+South Asian (Iran Neolithic West Eurasian+AASI+some Steppe type West Eurasian)+Oceanian/Papuan+additional West Asian or European (mainly in the case of some Muslim SE Asians and Filipinos)/Han admixture (from recent Chinese migrations, specially in the case of Thailand).


    Edit: yes, I am utilizing G25 for these models.
    Last edited by Tsakhur; 08-17-2020 at 07:13 AM.

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    If you are using G25 for SE Africans it's best to use Natufian and also Tur_Barcin (ANF) or Levant_N since it's a combination of both.I would assume SE Africans who are Cushitic admixed excluding the Iraqw(they are cushites) probably have more West Eurasian ancestry than the average Malay or Filipino
    Drobbah_scaled
    Target: Drobbah_scaled
    Distance: 1.2698% / 0.01269848 | ADC: 0.25x
    31.0 KEN_Pastoral_N
    26.4 KEN_Pastoral_N_Elmenteitan
    18.4 TZA_PN
    12.0 KEN_HyraxHill_2300BP
    10.6 KEN_Pastoral_IA

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    Quote Originally Posted by drobbah View Post
    If you are using G25 for SE Africans it's best to use Natufian and also Tur_Barcin (ANF) or Levant_N since it's a combination of both.I would assume SE Africans who are Cushitic admixed excluding the Iraqw(they are cushites) probably have more West Eurasian ancestry than the average Malay or Filipino
    Yes I am utilizing G25. What specific Levant Neolithic population should I used: Levant_JOR_MBA, Levant_PPNB or Levant_Megiddo_IA, etc?

    Also is it suitable to utilize UG_Munsa_500BP, COG_NgongoMbata, Dinka, ETH_4500_BP and Bedzan as African source populations?

    Do you know if the Luo, Luhya, Bantu_Kenya and Bantu S.E., Hadza Cushitic admixed or not?

    I believe your assumption is correct regarding Cushitic admixed SE Asians being more Western than the average Malay or Filipino. Nonetheless, I believe that some Thai G25 samples have similar amounts of West Eurasian ancestry to the Sengwer (are they also Cushitic mixed?).

    I feel that the Indian/South Asian ancestry in SE Asia is a bit analogous to the Cushitic ancestry in non-Horner SE Africa.

    Im not sure if Burma and Thailand has similar amounts of West Eurasian ancestry to Kenya and Tanzania or less, but it would be intriguing and fun to determine this.
    Last edited by Tsakhur; 08-17-2020 at 07:49 AM.

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    It's probably best to use Natufian or the Neolithic Levant samples (PPNB/PPNC) the others you mentioned are not Neolithic.

    Dinka,Mota,Yoruba,Ken_LSA,Taforalt and those old ZAF samples is what I usually run for these SE Africans.

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    Quote Originally Posted by drobbah View Post
    It's probably best to use Natufian or the Neolithic Levant samples (PPNB/PPNC) the others you mentioned are not Neolithic.

    Dinka,Mota,Yoruba,Ken_LSA,Taforalt and those old ZAF samples is what I usually run for these SE Africans.
    I see. Thanks.

    Does Ken_LSA and Tarofalt contain West Eurasian ancestry or is it "purely African"?

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    Quote Originally Posted by Tsakhur View Post
    I see. Thanks.

    Does Ken_LSA and Tarofalt contain West Eurasian ancestry or is it "purely African"?
    I don't think Ken_LSA has West Eurasian ancestry but Taforalt is majority Natufian-like but has deep ANA African ancestry.Since we don't have pure ANA samples they are the next best thing

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    Ken_LSA and Mota both definitely have Eurasian ancestry. Mota has some very old and non-differentiated Eurasian-like ancestry. I'm almost entirely sure its Eurasian, because it carries proportional amounts of Neanderthal Dna while Ken_LSA has some recent pastoralist ancestry on on top of its Mota-like ancestry.

    Mota can be modeled in qpAdm very well as 60-66 percent Dinka, 24-27 percent South African and 13-17 percent UstIshim.

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    Quote Originally Posted by Mnemonics View Post
    Ken_LSA and Mota both definitely have Eurasian ancestry. Mota has some very old and non-differentiated Eurasian-like ancestry. I'm almost entirely sure its Eurasian, because it carries proportional amounts of Neanderthal Dna while Ken_LSA has some recent pastoralist ancestry on on top of its Mota-like ancestry.

    Mota can be modeled in qpAdm very well as 60-66 percent Dinka, 24-27 percent South African and 13-17 percent UstIshim.
    I admit I am a bit of a novice on this subject but I think we ought to be careful about drawing too many conclusions about this “deep” Neandertal affinity in SSA (I am not talking about the obvious examples of Eurasian gene flow), particularly since we’re still learning about the nature of this affinity. Some of it may be due to pre-OOA gene flow from AMH into Neanderthals but I’ve heard rumors that the Reich lab is planning to publish some interesting findings on this subject in early 2021 if not sooner.

    I am not sure if this qpAdm result is that convincing. I know it’s not recommended to mix modern and ancient populations, especially populations like Ust-Ishim due to their basal nature. Paleolithic aDNA from NE Africa is a huge gap that needs to be filled.

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    It is generally fine to mix Moderns and Ancients when using transversion snps as they are much less likely to be damaged than transition snps.

    I wouldn't be so sure about it if the signal wasn't so robust. African population history is very complex and some African groups (East Africans and West Africans) share a common ancestor with Eurasians to the exclusion of other Africans (Pygmies, and San). However, using F4ratios it is pretty easy to distinguish between common pre-OOA ancestry and Eurasian ancestry.

    Eurasian African X Chimp/San : Eurasian Africa Eurasian2 Chimp/San

    If you use the above F4 ratio, and the Eurasians selected have similar levels of Neanderthal admixture, you can distinguish between African and Eurasian ancestry by changing the African from the most basal African groups to those closest to Eurasians. If the Eurasian affinity stays when you move past the population you are examining (phylogenetically), than it almost always reflected in Neanderthal F4Ratios.

    This also works pretty well for Eurasians too.

    In fact, using this method, it seems like the African affinity found in some Eurasians seems to have come, at least partially, from some very deep population because It is distinguished reasonably well by including African Hunter-Gatherer populations.

    Maybe the original Iberomaurusian paper was right about them having something Hadza-like.
    Last edited by Mnemonics; 08-22-2020 at 03:46 AM.

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    Quote Originally Posted by Mnemonics View Post
    Ken_LSA and Mota both definitely have Eurasian ancestry. Mota has some very old and non-differentiated Eurasian-like ancestry. I'm almost entirely sure its Eurasian, because it carries proportional amounts of Neanderthal Dna while Ken_LSA has some recent pastoralist ancestry on on top of its Mota-like ancestry.

    Mota can be modeled in qpAdm very well as 60-66 percent Dinka, 24-27 percent South African and 13-17 percent UstIshim.
    Interesting. Is the Eurasian ancestry in Ken_LSA and Mota, more Eastern or Western Eurasian or is it just too ancient to be classify as one of the two categories and just its own unique branch?

    How do you run qpadm or interpret the results btw? I don't know how to do it.
    Last edited by Tsakhur; 08-24-2020 at 06:44 PM.

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