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Thread: Experimental K12 "Deep" Calculator for Africans and West Eurasians

  1. #71
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    ZanzibarSultanate Iran Southern Sudan India Nigeria ZanzibarSultanate
    This is the only calculator via nMonte that can accurately gauge African ancestry in high Basal populations (East Iranics etc) such as in the Makrani (~15%) instead of the 3-4% you can squeeze out using other models, when adding an Ancestral Indian Simulation. High Iran_N/Hotu seems to throw African admixture out the window..I saw Awale post about this regarding Copts (basal stuff etc) quite a while back. Using G25 as what it is, a PCA, you can see that individuals plot in the correct positions on Africa PCAs, but nMonte can skewer this perception. The calculator also picks up Ancestral North African in the right ball park (close to half of IBM total, instead of a 1/3 or whatever). The only issue is Ancestral North African which either pulls Maghrebis closer to SSAs or the other way around - guess we won't know until actual samples are found.
    Last edited by ThaYamamoto; 08-14-2020 at 06:06 PM.

  2. #72
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    Mine

    Target: JFWinstone_scaled
    Distance: 2.1324% / 0.02132404
    41.0 POL_Globular_Amphora
    37.6 Yamnaya_RUS_Samara
    6.4 JPN_Jomon_3800BP
    4.8 Malaysia_LN_2550BP
    3.8 Sino-Tibetan
    3.6 Basal_West_African
    0.8 Baltic_LTU_Narva
    0.6 Basal_Central-West_African
    0.6 ITA_Villabruna
    0.4 Basal_Central-East_African
    0.2 Ancestral_N_African
    0.2 Basal_East_African

    Mum

    Target: JFWinstoneMum_scaled
    Distance: 1.8669% / 0.01866922
    28.2 POL_Globular_Amphora
    25.6 Yamnaya_RUS_Samara
    12.8 JPN_Jomon_3800BP
    10.8 Malaysia_LN_2550BP
    7.0 Basal_West_African
    6.6 Sino-Tibetan
    2.8 PAK_Saidu_Sharif_H_o
    2.2 Basal_Central-West_African
    1.4 Basal_East_African
    1.2 Papuan
    0.6 KAZ_Botai_5200BP
    0.4 Ancestral_N_African
    0.4 ITA_Villabruna

    Dad

    Target: JFWinstoneDad_scaled
    Distance: 4.1978% / 0.04197823
    56.2 POL_Globular_Amphora
    40.8 Yamnaya_RUS_Samara
    3.0 Baltic_LTU_Narva
    Ethnogene: 51.4% NW European, 21.6% W European, 10.1% Southeastern African, 9.5% Southeast Asian, 4.4% South Asian, 2% Scandinavian, 1% East African
    Papertrail @ 2xggrandparents: 37.5% London, 25% Dorset, 25% Mauritius, 6.25% Netherlands, 6.25% Hampshire

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     ThaYamamoto (08-17-2020)

  4. #73
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    Interesting work!

    I tried with the Basal component, removing Villabruna and Ancient Arabian

    Target: Helves_scaled
    Distance: 5.5246% / 0.05524613
    60.2 Caspian
    26.4 ITA_Villabruna
    13.4 Basal_Eurasian

    Removed Caspian, Yamnaya and UstIshim and added MA1 + AG3. But doesn't seem to work that deep. It's way off Davids Basal-rich run he made a couple years ago.

    Target: Helves_scaled
    Distance: 15.5835% / 0.15583481
    44.0 RUS_MA1:MA1
    33.4 ITA_Villabruna
    21.0 Basal_Eurasian
    1.6 Basal_West_African
    Last edited by Helves; 08-19-2020 at 01:24 AM.

  5. #74
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    Quote Originally Posted by K33 View Post
    I tried to create a Basal Eurasian component-- and I was able to-- but it only looked right for Natufians, Arabians, and East Africans. I was unable to model TUR_Barcin with the BE component, and so Barcin has to stay in as an anchor.

    When they were first discovered, Natufians were thought to have ~50% Basal Eurasian ancestry, and Barcin something like 44%. Then in an updated paper it was claimed Barcin only had 14% BE (so by extension Natufians would have around 15-18%. Finally in the Dzudzuana paper they pegged Natufians at ~32% BE (including the BE within Taforalt), with Barcin at 26-28% BE. My theory on what's going on with these huge estimate differences, is that since Ust_Ishim and Basal African/Basal Eurasian have no particular affinity to either East or West Eurasians, the commingling of Basal + Ust Ishim ancestries (especially if they admixed in the Paleolithic) is making it hard for geneticists to separate them.
    I tried doing something similar some time back. Anatolians did pick some of that simulated Basal, but the fit still wasn't right on Scaled.
    Meast.png

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    Question:

    In this ancient model I added some of the basal components and it really improved the fit of the model, but something remarkable happens when I do the following. This first result is with the Basal West_African and Central_African added to it in order to function as a Sub Saharan African proxy, I get a great fit with it (Distance: 1.2583%), but what happens is the following: Here in this model I get this chunk of Levantine_Farmer (which I get in many models). But when I add Basal_Eurasian to this model 2 things happen: 1. The fit even gets better and 2. the Levantine_Farmer component drastically decreased, why is that so?

    Target: Adam_Scaled
    Distance: 1.2583% / 0.01258335
    38.6 Early_European_Farmer
    31.0 Iberomaurusian
    11.4 Early_Levantine_Farmer
    9.4 Steppe_Pastoralist
    2.8 Iran_Neolithic
    2.6 Western_Hunter-Gatherer
    2.4 Basal_Central/West_African
    1.8 Caucasus_Hunter-gatherer


    (Adding Basal_Eurasian):

    Target: Adam_Scaled
    Distance: 1.0779% / 0.01077924
    38.8 Early_European_Farmer
    31.4 Iberomaurusian
    8.4 Western_Hunter-Gatherer
    7.6 Steppe_Pastoralist
    6.2 Iran_Neolithic
    3.4 SSA (Basal Central_African/West_African)
    2.4 Basal_Eurasian
    1.0 Caucasus_Hunter-gatherer
    0.8 Early_Levantine_Farmer

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  8. #76
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    Quote Originally Posted by Adamm View Post
    Question:

    In this ancient model I added some of the basal components and it really improved the fit of the model, but something remarkable happens when I do the following. This first result is with the Basal West_African and Central_African added to it in order to function as a Sub Saharan African proxy, I get a great fit with it (Distance: 1.2583%), but what happens is the following: Here in this model I get this chunk of Levantine_Farmer (which I get in many models). But when I add Basal_Eurasian to this model 2 things happen: 1. The fit even gets better and 2. the Levantine_Farmer component drastically decreased, why is that so?

    Target: Adam_Scaled
    Distance: 1.2583% / 0.01258335
    38.6 Early_European_Farmer
    31.0 Iberomaurusian
    11.4 Early_Levantine_Farmer
    9.4 Steppe_Pastoralist
    2.8 Iran_Neolithic
    2.6 Western_Hunter-Gatherer
    2.4 Basal_Central/West_African
    1.8 Caucasus_Hunter-gatherer


    (Adding Basal_Eurasian):

    Target: Adam_Scaled
    Distance: 1.0779% / 0.01077924
    38.8 Early_European_Farmer
    31.4 Iberomaurusian
    8.4 Western_Hunter-Gatherer
    7.6 Steppe_Pastoralist
    6.2 Iran_Neolithic
    3.4 SSA (Basal Central_African/West_African)
    2.4 Basal_Eurasian
    1.0 Caucasus_Hunter-gatherer
    0.8 Early_Levantine_Farmer
    isn't it because natufians are themselves partially basal eurasian ? And maybe it gets better because basal eurasians were not partially iberomaurusian like natufians

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  10. #77
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    Quote Originally Posted by Nassbean View Post
    isn't it because natufians are themselves partially basal eurasian ? And maybe it gets better because basal eurasians were not partially iberomaurusian like natufians
    Yeah but check the difference, the Basal Eurasian only absorbed 2% while the 11% Natufian almost totally disappeared. Why is that so?

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  12. #78
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    Quote Originally Posted by Adamm View Post
    Yeah but check the difference, the Basal Eurasian only absorbed 2% while the 11% Natufian almost totally disappeared. Why is that so?
    mainly redistributed into iran neolithic and WHG or maybe I'm wrong idk

  13. #79
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    K33, have you considered adding these to the calculator?

    Code:
    AncestralIndianSouth_scaled,-0.007017607,-0.247268894,-0.229976338,0.16563825,-0.035368871,0.064331863,-0.015188881,0.027727614,0.147380455,0.101064071,-0.004664075,-0.004333522,0.003228897,0.026031903,-0.047720864,-0.045200255,0.010093749,0.000906224,0.000245098,0. 039040136,0.009429353,0.024010206,-0.003068505,0.015983546,-0.010868946
    
    AncestralIndianNorthWest_scaled,0.058062278,-0.24745847,-0.325699695,0.273535685,-0.119223593,0.177284363,0.005596483,0.058361388,0. 170617118,0.13535108,-0.00361402,0.035724435,-0.030872625,0.03748403,-0.013375715,-0.129868563,0.005831905,-0.02091509,-0.021039598,0.054171475,0.001207383,0.0099081,0.01 941486,0.05655002,-0.064804895

  14. #80
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    Ancestry*

    Target: Gerald_scaled
    Distance: 3.1066% / 0.03106616
    53.2 POL_Globular_Amphora
    46.2 Yamnaya_RUS_Samara
    0.4 Pre-Pastoralist
    0.2 TUR_Barcin_N

    23/me

    Target: Gerald_scaled
    Distance: 3.9814% / 0.03981430
    54.6 POL_Globular_Amphora
    44.8 Yamnaya_RUS_Samara
    0.4 Pre-Pastoralist
    0.2 Ancestral_N_African

    I don't know what any of this indicates but here it is.

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