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Thread: Genomic History of Neolithic to Bronze Age Anatolia, N Levant, and S Caucasus 2020

  1. #51
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    Over on the Eurogenes blog a guy has posted these results for the same samples as in the above post. He got more IRN_N type ancestry for them.

    Target: join@AZE_Caucasus_lowlands_LN:MTT001
    Distance: 2.4902% / 0.02490202
    57.4 IRN_Hajji_Firuz_C
    31.2 TUR_Tepecik_Ciftlik_N
    8.0 GEO_CHG
    2.4 Levant_PPNB
    1.0 RUS_Progress_En
    0.0 RUS_Darkveti-Meshoko_En
    0.0 RUS_Tyumen_HG


    Target: join@AZE_Caucasus_lowlands_LN:MTT001
    Distance: 2.4902% / 0.02490202
    57.4 IRN_Hajji_Firuz_C
    31.2 TUR_Tepecik_Ciftlik_N
    8.0 GEO_CHG
    2.4 Levant_PPNB
    1.0 RUS_Progress_En
    0.0 RUS_Darkveti-Meshoko_En
    0.0 RUS_Tyumen_HG

    Target: AZE_Caucasus_lowlands_LC
    Distance: 5.6410% / 0.05641048
    80.0 IRN_Hajji_Firuz_C
    14.8 Levant_PPNB
    5.2 RUS_Progress_En
    0.0 GEO_CHG
    0.0 RUS_Darkveti-Meshoko_En
    0.0 RUS_Tyumen_HG
    0.0 TUR_Tepecik_Ciftlik_N

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  3. #52
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    G2a2b1 M406> FGC5081

    Byzantine Empire Empire of Trebizond Greek Macedonia Greece
    Quote Originally Posted by J Man View Post
    Over on the Eurogenes blog a guy has posted these results for the same samples as in the above post. He got more IRN_N type ancestry for them.

    Target: join@AZE_Caucasus_lowlands_LN:MTT001
    Distance: 2.4902% / 0.02490202
    57.4 IRN_Hajji_Firuz_C
    31.2 TUR_Tepecik_Ciftlik_N
    8.0 GEO_CHG
    2.4 Levant_PPNB
    1.0 RUS_Progress_En
    0.0 RUS_Darkveti-Meshoko_En
    0.0 RUS_Tyumen_HG


    Target: join@AZE_Caucasus_lowlands_LN:MTT001
    Distance: 2.4902% / 0.02490202
    57.4 IRN_Hajji_Firuz_C
    31.2 TUR_Tepecik_Ciftlik_N
    8.0 GEO_CHG
    2.4 Levant_PPNB
    1.0 RUS_Progress_En
    0.0 RUS_Darkveti-Meshoko_En
    0.0 RUS_Tyumen_HG

    Target: AZE_Caucasus_lowlands_LC
    Distance: 5.6410% / 0.05641048
    80.0 IRN_Hajji_Firuz_C
    14.8 Levant_PPNB
    5.2 RUS_Progress_En
    0.0 GEO_CHG
    0.0 RUS_Darkveti-Meshoko_En
    0.0 RUS_Tyumen_HG
    0.0 TUR_Tepecik_Ciftlik_N
    Iran Hajji Firuz is a very mixed sample. Tepecik Ciftlik also..
    Target: Ioannis_scaled
    Distance: 1.5780% / 0.01578004
    40.2 TUR_Ikiztepe_LC
    32.4 Kura-Araxes_ARM_Kaps
    16.2 Levant_Baqah_BA
    11.2 Iberia_Northeast_Empuries2


    Target: Ioannis_scaled
    Distance: 2.8082% / 0.02808208
    67.2 Greek_Trabzon
    24.2 Samaritan
    7.4 Georgian_Imer
    1.2 Sardinian

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  5. #53
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    G2a2b1 M406> FGC5081

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    Quote Originally Posted by J Man View Post
    That is actually quite interesting. It is a shame that there are no Y-DNA haplogroups reported from these samples. At this point it is tempting to link the expansion of G2a clades into the Caucasus with groups such as the Shomu-Shulaveri and possibly certain J2a clades as well given their IRN_Ganj_Dareh_N ancestry as well.
    Agree. As a Pontic Greek My self we are mostly a mix of ANF(G2a) and Maykop-Kura Araxes(J2a) lineages. Eastern Anatolia and Caucasus are mixing populations between these 2 lineages.
    Target: Ioannis_scaled
    Distance: 1.5780% / 0.01578004
    40.2 TUR_Ikiztepe_LC
    32.4 Kura-Araxes_ARM_Kaps
    16.2 Levant_Baqah_BA
    11.2 Iberia_Northeast_Empuries2


    Target: Ioannis_scaled
    Distance: 2.8082% / 0.02808208
    67.2 Greek_Trabzon
    24.2 Samaritan
    7.4 Georgian_Imer
    1.2 Sardinian

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  7. #54
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    Quote Originally Posted by misnomer View Post
    Merged the eigenstrat file and ran qpAdm on the well woman. almost no sintashta, but mtDna H2a3 would suggest that a miniscule amount is present.

    left pops:
    Alalakh_MLBA_outlier

    Uzbekistan_BA_Dzharkutan1: 83 +- 4.5
    Russia_MLBA_Sintashta: 3.3 +- 3.1
    Kyrgyzstan_BA_Aygirdjal: 13.7 +- 4.9
    pvalue: 0.4488

    Nested Model
    Uzbekistan_BA_Dzharkutan1: 84
    Kyrgyzstan_BA_Aygirdjal: 16
    p-value: 0.4356 (no pvalue change without sintashta)

    Nested model 2
    Uzbekistan_BA_Dzharkutan1: 93.1
    Russia_MLBA_Sintashta: 6.9
    pvalue: 0.0685 (big pvalue drop)

    Result file https://pastebin.com/K4b8Sj60

    The mtDna is H2a3, only ancient match is from czech corded ware and britain_eba. This adds to the Narsimhan paper evidence that the steppe related ancestry in south and central asia in BA was mostly female mediated.

    This woman may or may not be related to the mitannis but imo she was surely connected to the flow of material and domesticated animals from S/SC asia to near east.
    In GD she picks up 7-10% Yamnaya Samara, she needs a mix of a BMAC source and an earlier source or an IVC source, her ANF interestingly was around the same level or slightly lower than many in the BMAC cluster, this after picking up Steppe ancestry, she also has 3-3.5% AASI, She prefers Zevakinsky LBA and Chemurchek EBA, you can verify on qpAdm which one. Though 20% of her ancestry is from the Steppe.


    "sample": "Custom:TUR_Alalakh_MLBA_o",
    "fit": 1.5607,
    "UZB_Sappali_Tepe_BA": 60,
    "IRN_Shahr_I_Sokhta_BA1": 20,
    "KAZ_Zevakinskiy_LBA": 20,





    Target: TUR_Alalakh_MLBA_o
    Distance: 1.4460% / 0.01445992
    76.2 UZB_Sappali_Tepe_BA
    18.0 MNG_Chemurchek_EBA_2
    5.8 IRN_Shahr_I_Sokhta_BA2



    "sample": "Custom:TUR_Alalakh_MLBA_o",
    "fit": 2.8844,
    "IRN_Ganj_Dareh_N": 54.17,
    "RUS_AfontovaGora3": 15,
    "Anatolia_Barcin_N": 14.17,
    "GEO_CHG": 13.33,
    "Simulated_AASI": 3.33,
    "WHG": 0,


    "sample": "UZB_Sappali_Tepe_BA:Average",
    "fit": 1.8414,
    "IRN_Ganj_Dareh_N": 65.83,
    "Anatolia_Barcin_N": 16.67,
    "GEO_CHG": 11.67,
    "RUS_AfontovaGora3": 4.17,
    "Simulated_AASI": 1.67,




    Distance: 0.37144915582741506%

    TKM_Gonur1_BA: 50.8%
    TKM_Geoksyur_En: 11.9%
    PAK_Udegram_IA: 9.2%
    IRN_HotuIIIb_Meso: 8.1%
    UZB_Sappali_Tepe_BA: 6.5%
    Yamnaya_UKR: 4.0%
    Yamnaya_KAZ_Karagash: 3.2%
    IRN_Ganj_Dareh_N: 2.0%
    KEN_Pastoral_N: 1.9%
    VUT_150BP: 1.4%
    RUS_Sintashta_MLBA_o1: 0.9%
    Other: 0.0%

    I avoided the main Gonur cluster because there is a mild outlier (1793) like her on there.


    "sample": "TKM_Gonur1_BA:I1793",
    "fit": 3.4022,
    "UZB_Sappali_Tepe_BA": 65,
    "TKM_Gonur2_BA": 22.5,
    "CustomGroup_CentralSteppeMLBA": 12.5,
    Last edited by pegasus; 05-30-2020 at 12:02 AM.

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  9. #55
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    Quote Originally Posted by Johnny ola View Post
    Iran Hajji Firuz is a very mixed sample. Tepecik Ciftlik also..
    Do both Iran Hajji Firuz and Tepecik Ciftlik have a lot of ANF ancestry? I am thinking that they likely do.

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  11. #56
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    Quote Originally Posted by J Man View Post
    Do both Iran Hajji Firuz and Tepecik Ciftlik have a lot of ANF ancestry? I am thinking that they likely do.
    HajjiFiruz_CA is ~50% ANF, Tepecik_N ~75-80%
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

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  13. #57
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    Quote Originally Posted by Johnny ola View Post
    Iran Hajji Firuz is a very mixed sample. Tepecik Ciftlik also..
    So this guy below is a late Shulaveri-Shomu lad?...His Y-DNA is G1.

    Target: AZE_Caucasus_lowlands_LC:ALX002
    Distance: 5.1904% / 0.05190383
    50.8 TUR_Barcin_N
    38.0 IRN_Ganj_Dareh_N
    5.8 GEO_CHG
    4.4 Levant_Natufian
    1.0 RUS_Karelia_HG

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  15. #58
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    Quote Originally Posted by J Man View Post
    So this guy below is a late Shulaveri-Shomu lad?...His Y-DNA is G1.

    Target: AZE_Caucasus_lowlands_LC:ALX002
    Distance: 5.1904% / 0.05190383
    50.8 TUR_Barcin_N
    38.0 IRN_Ganj_Dareh_N
    5.8 GEO_CHG
    4.4 Levant_Natufian
    1.0 RUS_Karelia_HG
    Compare to an old F3 outgroup nmonte model of Hajji_Firuz_CA

    Iran_Hajji_Firuz
    ANF: 44.2%
    "Mentese_N" 26.05
    "Peloponnese_N" 11.35
    "Boncuklu_N" 6.8

    INF: 39.8%
    "Iran_SehGabi_LN" 21.7
    "Turkmenistan_N" 18.1

    "Satsurblia" 9.95
    "Levant_N" 4.55
    "AG3" 1.5
    "distance%=0.0782 / distance=0.000782"
    Columns: Barcin_N, Iran_N, Natufian, Kotias, Taforalt, MA1, Anzick_Kennewick, Iron_Gates_HG, EHG, Ust_Ishim
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

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  17. #59
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    The dates do not seem to line up very well but it could be possible that some of the Arslantepe samples descend from Kura-Araxes pastoralists.

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  19. #60
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    J-Z482>Y15222
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    R-Z36>Y156527

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    Quote Originally Posted by J Man View Post
    The dates do not seem to line up very well but it could be possible that some of the Arslantepe samples descend from Kura-Araxes pastoralists.
    When all the data is finished from the three papers I will update the J2 history thread and take a deep look into the paper to see if what were seeing is K-A, the Chalcolithic aged samples shouldn’t be. Its early EBA that would be contenders.
    My Y Line: J2a-L210>Z489>Z482>Y15222

    My Maternal Y: R1b-U152>Z36>Y156527

    Other Y lines: 3x Great Grandfather on Maternal side: J2a-S25258>SK1336, 5x Great Grandfather on Maternal side: E-V13> A7135, 6x Great Grandfather on Maternal side: J1-Z2331>L829

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