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Thread: Explorations with K13-Derived G25 Sims

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  1. #1
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    Explorations with K13-Derived G25 Sims

    Per my Moriopoulos G25 Collection thread:

    Many simulated G25 coords have been made over the years to help fill in gaps in the ancient DNA record. I make use of DMXX's excellent AASI sims all the time. I have also recently made very good use of Genoplot's impressive K13 to G25 simulation tool. This is experimental and isn't a replacement for real G25 coords, obviously, but for elementary plotting, distance runs, and modelling, I think it's really cool. Although G25 is fairly exhaustive, there are still a lot of interesting groups missing, some of which do have K13 representation. Naturally, I capitalized on this "better-than-nothing" opportunity to "fill in the gaps" and maybe got a little carried away! I've converted hundreds of K13 coords to G25 sims this way. My Greek friend 23abc has also joined me in this venture. This has increased my G25 collection by ~600 individuals. Mandaeans, Karaites, Tigrinya, oh my!
    This thread is intended to be a place to explore these sims. I'll start with Africa. I looked for some actual Tigrinya since I found the ethnically-unspecified Eritrean samples annoying. A Tigrinya individual has sent me their own G25 coords for me to compare to these sims. They're very close. The sims are the aqua dots and the real Tigrinya is the red dot:

     


    Distance to: Tigrinya_Eritrea_K13
    0.02232515 Agaw
    0.02261900 Amhara
    0.02421626 Tigray_Ethiopia
    0.02422241 Kenya_Early_Pastoral_N
    0.02550496 Tigrinya_Eritrea
    0.02553081 Ethiopian_Jew
    0.02637353 Afar_Ethiopia
    0.03016658 Eritrean
    0.03910138 Beja_Hadendowa
    0.04378228 Nubia_Medieval_Christian_Era_Kulubnarti_R
    0.04900001 Nubian_Mahas
    0.05009333 Sudanese_Arab_Ja'alin
    0.05138313 Nubia_Medieval_Christian_Era_Kulubnarti_S
    0.05287109 Beja_Beni-Amer
    0.05657582 Nubian_Danagla
    0.05820396 Sudanese_Arab_Shaigia
    0.05933700 Nubian_Halfawi
    0.06304336 Oromo_Ethiopia
    0.06905448 Tanzania_PN_o
    0.06988519 Kenya_Pastoral_N_o
    0.07904750 Kenya_Pastoral_N_Elmenteitan
    0.08115653 Sudanese_Arab_Shaigia_o1
    0.08195363 Tanzania_PN
    0.08483340 Kenya_Hyrax_Hill_2300BP
    0.08667526 Sudanese_Arab_Batahin

    I also have a couple of Mauritanians. One has real G25 coords and the other is a K13 sim. Both are Beidan ("white Moors"), so we're talking genetically West Eurasian Mauritanians. Same scheme below (aqua dot is K13 sim, red dot is sample with real coords):

     


    Distance to: Mauritanian_Beidan_K13
    0.03095470 Berber_Morocco_Central_Atlas_Tamazight_Errachidia
    0.03215280 Moroccan_Casablanca
    0.03379533 Moroccan_Ouarzazate
    0.03504338 Saharawi
    0.03906774 Berber_Algeria_Gourara_Timimoun
    0.03917026 Berber_Algeria_Mozabite
    0.04318470 Moroccan_Errachidia
    0.05018969 Moroccan
    0.05152009 Berber_Morocco_Shilha_Tiznit
    0.05154277 Tunisian_Jendouba
    0.05350724 Berber_Morocco_Shilha
    0.05369794 Algerian_Algiers
    0.05606520 Berber_Morocco_Central_Atlas_Tamazight
    0.05791549 Mauritanian_Beidan
    0.06170688 Tunisian_Tunis
    0.06279844 Sardinia_CA_(North_African_Profile)
    0.06352254 Guanche_Canary_Islands
    0.06518367 Iberia_Central_CA_(North_African_Profile)
    0.06543630 Berber_Mali_Tuareg
    0.06612137 Berber_Tunisia_East_Zenati_Tamezret
    0.06774836 Algerian
    0.06996457 Berber_Tunisia_East_Zenati_Sened
    0.07119766 Tunisian_Arab_Dou
    0.07162097 Moroccan_Oujda
    0.07322291 Berber_Tunisia_East_Zenati_Zraoua

    More to come...
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  3. #2
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    I'm not finding the simulations so close in my real world. I added myself and my parents to your G25 scaled list with real Davidski coordinates. None of the kits showed in the top 25. So I ran them will only us in them.


    Distance to: PLogan-K13-sim_scaled
    0.02810338 Father_scaled
    0.04086291 Mother_scaled
    0.04489678 PLogan_scaled

    Distance to: Father-K13-sim_scaled
    0.02858987 Father_scaled
    0.04090972 Mother_scaled
    0.04514816 PLogan_scaled

    Distance to: Mother-K13-sim_scaled
    0.02220189 Father_scaled
    0.02475657 Mother_scaled
    0.03002239 PLogan_scaled

    Simulations leave me skeptical, but I guess they're better than nothing.

    BTW: Not knocking your post in any way, just contributing per the nature of the thread in exploring simulations.
    Last edited by PLogan; 03-08-2022 at 11:50 PM.

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  5. #3
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    Quote Originally Posted by PLogan View Post
    I'm not finding the simulations so close in my real world. I added myself and my parents to your G25 scaled list with real Davidski coordinates. None of the kits showed in the top 25. So I ran them will only us in them.
    That doesn't surprise me. There are a lot of Northern European groups in the list and they're so similar to each other that it would be easy to see how that could happen running a sim against real coords.

    ----

    Here's a sim of Saqqaq (aqua dot) on ENA + Amerind PCA:

     


    And on East Asian PCA:

     


    Distances:
    Distance to: Saqqaq_Paleo-Eskimo_K13_sim
    0.02483119 Shumilikha_EBA
    0.02936534 Shumilikha_EN
    0.03116552 Sokhter_NEBA
    0.03498294 Glazkovo_LNBA_o
    0.03567355 Makarovo_N
    0.03607432 Shamanka_EBA
    0.03661106 Mys_Uyuga_NEBA
    0.03667411 Chastaja_Padi_N
    0.03900621 Makrushino_LNBA
    0.03902575 Kirpichnyj_Saraj_N
    0.03917221 Khaptsagai_LNBA
    0.03948571 Sukhaja_Pad’_Buret’_EBA
    0.04028091 Gorodische_N
    0.04108454 Zhigalovo_LNBA
    0.04127575 Glazkovo_EBA
    0.04142387 Ust_Ida_EBA
    0.04143464 Ust-Ida_EBA
    0.04215738 Shishkino_BA
    0.04252414 Zapleskino_LNEBA
    0.04394841 Kurma_EBA
    0.04527739 Ust-Dolgoe_BA
    0.04619434 Zvjozdochka_BA
    0.04724805 Iushino_EN
    0.04953528 Shumilikha_MN
    0.05236355 Dzhylinda_Mesolithic
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  7. #4
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    unless there is a need to isolate/identify an unusual or atypical group or person what are the reasons for sim samples? Your last model which incorporated real profiles seems to be a better model than even generic averages. Forgive my ignorance on the matter.

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    Quote Originally Posted by JerryS. View Post
    unless there is a need to isolate/identify an unusual or atypical group or person what are the reasons for sim samples?
    It's a coarse method that allows us to identify how groups currently not represented in the G25 would roughly plot on a G25 PCA. It's obviously not a substitute for real G25 coordinates but still gives a fair portrait of basic populational affinity. As such I find it to be a very useful stopgap while we wait for these groups to be represented (or better represented) with real coords. It's not meant to be a fine-resolution method, just a fun experimental feature. It's probably best applied for averages rather than for individuals, and is definitely geared toward West Eurasians. That said, most people I know who have compared their own real G25 coordinates to their K13 sim analogues are surprised by how closely the two points plot. There is usually only a marginal offset, almost acting like a lower resolution of the actual coords. Some examples below, real coords (light green dot) and K13 sim (aqua diamond):

    My brother:
     


    My mother:
     


    My Cypriot friend (and AG member) Andrewid:
     


    And below is me-- my sim is worst I've seen so far in terms of the gap (somewhat ironically since my kit has better coverage than my bro's and mom's), but it's still in the neighborhood of where I actually plot (among Central Italians and mainland Greeks):

     


    So I'm pretty happy with it, especially for averages.
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  11. #6
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    Quote Originally Posted by Michalis Moriopoulos View Post
    It's a coarse method that allows us to identify how groups currently not represented in the G25 would roughly plot on a G25 PCA. It's obviously not a substitute for real G25 coordinates but still gives a fair portrait of basic populational affinity.

    I thought it would be useful to see how the simulations plot in aggregate for a group of samples as opposed to individuals. Here are 10 samples selected from the large Iranian data set that happen to have G25 coordinates as well as Eurogenes K13 and HarappaWorld results in Genoplot. They're labeled as 'Kurdish' out of convenience as I needed names for the custom groups so they could be plotted as groups rather than individual samples. They are, in fact, close to Kurdish samples, so they may well be Kurds in reality.


    Here is how these 10 plot in relationship to other West Asian groups using the Genoplot West Asian preset (I've highlighted 11AM180 for all 3 types)




    And here are all 10 samples zoomed in with shading for each type of sample to illustrate overlap between the sets


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    Last edited by Ajeje Brazorf; 03-10-2022 at 02:02 PM.

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    Thank you, Ajeje


    Target: JMcB_scaled
    Distance: 1.1875% / 0.01187452 | ADC: 0.5x RC

    48.8 English_simulated
    16.8 French_Normandy_simulated
    11.4 Scottish_Southwest_simulated

    11.0 French_Aquitaine_simulated
    7.8 Dutch_South_simulated
    4.2 German_Saarland_simulated





    Distance to: JMcB_scaled
    0.01545184 Dutch_South_simulated
    0.01766771 English_simulated

    0.01846232 Flemish_simulated
    0.01873358 English_Midlands_simulated
    0.01920031 English_Southwest_simulated
    0.01990873 Scottish_Southwest_simulated
    0.02037054 English_Southeast_simulated
    0.02108962 French_Normandy_simulated
    0.02199031 Irish_Munster_simulated
    0.02246063 German_Thuringia_Central_simulated
    0.02269457 Irish_Connacht_simulated
    0.02351206 Irish_Ulster_simulated
    0.02363921 German_West_Bohemia_simulated
    0.02368118 German_Schleswig-Holstein_simulated
    0.02421153 German_Saarland_simulated
    0.02443126 German_South_Hesse_simulated
    0.02525898 German_simulated
    0.02552546 French_Brittany_simulated
    0.02570860 German_North_Hesse_simulated
    0.02577251 German_North_Moravia_simulated
    0.02580353 German_Lower_Saxony_South_simulated
    0.02593229 Irish_Leinster_simulated
    0.02602568 German_Bavaria_Oberpfalz_simulated
    0.02620056 German_Saxony-Anhalt_South_simulated
    0.02657091 French_Northeast_simulated
    Last edited by JMcB; 03-10-2022 at 04:40 PM.
    Paper Trail: 42% English, 31.5% Scottish, 12.5% Irish, 6.25% German, 6.25% Sicilian & 1.5% French.
    LDNA(c): Britain & Ireland: 89.3% (51.5% English, 37.8% Scottish & Irish), N.W. Germanic: 7.8%, Europe South: 2.9% (Southern Italy & Sicily)
    BigY 700: I1-Z141 >F2642 >Y3649 >Y7198 (c.385 AD) >Y168300 (c.400 AD) >A13248 (c.860 AD) >A13252 (c.1050 AD) >FT81015 (c.1280 AD) >A13243 (c.1620 AD) >FT80854 (c.1700 AD) >FT80630 (1893 AD).

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    Some European sims have inflated WHG.


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  19. #10
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    Spain Andalucia Basque
    Target: gixajo_scaled
    Distance: 1.5199% / 0.01519879

    35.2 Spanish_Valencia_simulated
    18.6 Basque_France_simulated
    11.4 Portuguese_simulated
    7.4 Spanish_Castile-León_simulated
    7.4 Spanish_Castilla-La_Mancha_simulated
    7.0 French_South_simulated
    4.0 French_Brittany_simulated
    3.2 Spanish_Catalonia_simulated
    2.8 German_East_Prussia_Memelland_simulated
    2.0 Italian_Basilicata_simulated
    0.6 Tunisian_simulated
    0.4 Greek_Athens_simulated

    Target: gixajo_scaled
    Distance: 1.5206% / 0.01520595 | ADC: 0.25x RC

    34.2 Spanish_Valencia_simulated
    15.6 Basque_France_simulated
    15.2 Portuguese_simulated
    11.0 Spanish_Castilla-La_Mancha_simulated
    8.8 Spanish_Castile-León_simulated
    8.0 French_South_simulated
    2.8 Spanish_Catalonia_simulated
    2.6 German_East_Prussia_Memelland_simulated
    1.8 French_Brittany_simulated

    Target: gixajo_scaled
    Distance: 1.5694% / 0.01569388 | ADC: 0.5x RC

    29.4 Spanish_Valencia_simulated
    23.2 Spanish_Castile-León_simulated
    16.0 Basque_France_simulated
    15.4 French_South_simulated
    14.6 Spanish_Catalonia_simulated
    1.4 Spanish_Castilla-La_Mancha_simulated

    Target: gixajo_scaled
    Distance: 1.8201% / 0.01820088 | ADC: 1x RC

    42.2 Spanish_Valencia_simulated
    35.8 Spanish_Catalonia_simulated
    22.0 Spanish_Castilla-La_Mancha_simulated

    Distances

     
    Distance to: gixajo_scaled
    0.02008977 Spanish_Valencia_simulated
    0.02042877 Spanish_Catalonia_simulated
    0.02240016 Spanish_Castilla-La_Mancha_simulated
    0.02346309 Spanish_Aragon_simulated
    0.02408847 Spanish_Castile-León_simulated
    0.02538666 Portuguese_simulated
    0.02567780 Spanish_Andalusia_simulated
    0.02602907 Spanish_Cantabria_simulated
    0.02720836 Spanish_Galicia_simulated
    0.02865860 French_South_simulated
    0.02942712 Spanish_Murcia_simulated
    0.03125383 Spanish_Extremadura_simulated
    0.03250292 Italian_Aosta_Valley_simulated
    0.03290764 Swiss_Italian_simulated
    0.03371525 Italian_Piedmont_simulated
    0.03708889 French_Provence_simulated
    0.03725216 Italian_Trentino_simulated
    0.04281019 Basque_France_simulated
    0.04370748 French_Aquitaine_simulated
    0.04474865 Swiss_French_simulated
    0.04520865 Italian_Veneto_simulated
    0.04550948 German_Saarland_simulated
    0.04553413 French_Central_simulated
    0.04664007 Italian_Friuli_simulated
    0.04785786 Italian_Liguria_simulated

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