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Thread: List of ancient samples on GEDmatch

  1. #11
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    [cross post for the kit numbers]

    @David Powell (FamilyTreeDNA)
    Thresholds: 50 SNPs/1cM
    Code:
    M374116 (Scythian I0247) Largest segment = 2.5 cM Total of segments > 1 cM = 135.5 cM 98 matching segments
    M169040 (IRAN CHL I1665) Largest segment = 3.4 cM Total of segments > 1 cM = 139.7 cM 102 matching segments
    M258119 (IRAN CHL I1661) Largest segment = 3.4 cM Total of segments > 1 cM = 150.3 cM 108 matching segments
    M172663 (Afansievo Rise 511) Largest segment = 2.1 cM Total of segments > 1 cM = 152.0 cM 115 matching segments
    M145408 (EHG I0124 S) Largest segment = 5.7 cM Total of segments > 1 cM = 241.3 cM 149 matching segments
    M677694 (Satsurblia CHG) Largest segment = 3.7 cM Total of segments > 1 cM = 385.7 cM 269 matching segments
    M381564 (F38_Hasanlu, Iron Age Iran) Largest segment = 3.9 cM Total of segments > 1 cM = 491.0 cM 350 matching segments
    M967114 (I1290 IranN) Largest segment = 3.4 cM Total of segments > 1 cM = 651.3 cM 431 matching segments
    M091434 (I1584 AnatolianChL) Largest segment = 5.1 cM Total of segments > 1 cM = 721.5 cM 418 matching segments
    M277797 (RISE395_Sintashta) Largest segment = 5.4 cM Total of segments > 1 cM = 784.6 cM 511 matching segments
    M926386 (I1631 ArmeniaChL) Largest segment = 5.2 cM Total of segments > 1 cM = 831.6 cM 541 matching segments
    M115616 (I0867 LevantN) Largest segment = 4.4 cM Total of segments > 1 cM = 837.9 cM 514 matching segments
    M536324 (I1658 ArmeniaEBA) Largest segment = 5.1 cM Total of segments > 1 cM = 886.9 cM 561 matching segments
    M182163 (I1656 ArmeniaMLBA) Largest segment = 4.6 cM Total of segments > 1 cM = 924.1 cM 585 matching segments
    M655536 (I0231 Yamnaya) Largest segment = 4.4 cM Total of segments > 1 cM = 937.5 cM 608 matching segments
    M226800 (I0172 EsperstedtMN) Largest segment = 7.9 cM Total of segments > 1 cM = 948.9 cM 630 matching segments
    M324645 (I0112 BellBeaker) Largest segment = 6.8 cM Total of segments > 1 cM = 955.1 cM 598 matching segments
    M643041 (I0061 OleniyOstrov) Largest segment =4.4 cM Total of segments > 1 cM =956.7 cM 617 matching segments
    M754279 I0746 Anatolian EF Largest segment = 6.6 cM Total of segments > 1 cM = 963.9 cM 613 matching segments
    M512608 (I0100 LBK) Largest segment = 5.2 cM Total of segments > 1 cM = 979.5 cM 643 matching segments
    M572125 (I0054 LBK) Largest segment = 5.2 cM Total of segments > 1 cM = 983.7 cM 628 matching segments
    M608028 (RISE505_Andronovo) Largest segment = 5.1 cM Total of segments > 1 cM = 997.1 cM 655 matching segments
    M224345 (I0103 Corded Ware Germany) Largest segment = 4.9 cM Total of segments > 1 cM = 1,011.1 cM 657 matching segments
    M343758 (I0443 Yamnaya) Largest segment = 5.6 cM Total of segments > 1 cM = 1,013.3 cM 643 matching segments
    M313201 (I0099 HalberstadtLNBA) Largest segment = 5.0 cM Total of segments > 1 cM = 1,022.7cM 647 matching segments
    M936428 I0709 Anatolian EF Largest segment =6.6 cM Total of segments > 1 cM = 1,024.2 cM 654 matching segments
    M897077 I0707 Anatolian EF Largest segment = 5.7cM Total of segments > 1 cM = 1,059.3 cM 671 matching segments
    M547763 (I1300 Spain Chalcolithic) Largest segment = 6.1 cM Total of segments > 1 cM = 1134.4 cM 686 matching segments
    M411713 I1583 Anatolian EF Largest segment = 4.9 cM Total of segments > 1 cM = 1,137.6 cM 729 matching segments
    M411747 (Kotias) Largest segment = 14.7 cM Total of segments > 1 cM = 1,726.9 cM 587 matching segments
    Thanks to @Sangarius & @Mfa for the new kit numbers [well when I made the post in the code block]


    Original post
    Last edited by dp; 09-28-2016 at 07:48 PM.
    Grace and good eure and long prosperitee. [Lydg. Mum. Goldsmiths]

    ysearch/mitosearch id: atr94 GENBANK/ENA mtDNA id: KF703542 member ISOGG

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  3. #12
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    Gedmatch IDs:

    M311970 Bon002 Boncuklu, Central Anatolia 8279-7977 calBCE (10289-9987 BP)

    M380264 Rev5 Revenia, Central Greece 6438–6264 BCE (8448-8274 BP)
    M072869 Bar31 Barcin, Northwest Anatolia 6419-6238 BCE (8429-8248 ybp)
    M822045 Klei10 Kleitos, Central Greece 4230–3995 BCE (6240-6005 ybp)

    M197341 WC1 Wezmeh Cave, Central Zagros Iran 7455-7082 BCE (9465-9092 ybp)

    Bon002 had an unexpected eye color:
    Bon002 M311970 eye color prediction

    Try comparing the IBD of Bon004 at 100 SNPs and 1 cM with the others, and especially with:
    M677694 Satsurblia
    M603839 Kotias
    M115616 I0867 Levantine PPNB
    F999937 NE1 Starcevo
    F999916 Stuttgart LBK
    Last edited by Arame; 09-29-2016 at 04:08 AM.

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  5. #13
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    Quote Originally Posted by Arame View Post
    From Open Genomes


    Gedmatch IDs:

    M311970 Bon002 Boncuklu, Central Anatolia 8279-7977 calBCE (10289-9987 BP)

    M380264 Rev5 Revenia, Central Greece 6438–6264 BCE (8448-8274 BP)
    M072869 Bar31 Barcin, Northwest Anatolia 6419-6238 BCE (8429-8248 ybp)
    M822045 Klei10 Kleitos, Central Greece 4230–3995 BCE (6240-6005 ybp)

    M197341 WC1 Wezmeh Cave, Central Zagros Iran 7455-7082 BCE (9465-9092 ybp)
    Kits number not found on gedmatch
    Y haplogroup: R1b: L21+ DF13+ (L1335- DF21- DF49- FGC11134- L513- Z251- Z253- CTS1751- CTS3386- DF41- FGC5496- L371- MC14- S1026- S1051- S16264- Z16500- Z16502- Z255-)
    For my autosomal analyses, see Hidden Content

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  7. #14
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    yes he erased
    them god knows why
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    Adam

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  9. #15
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    Eurogenes K15 calculator used with Ancient Gedmatch samples:

    https://s9.postimg.org/h9vj9gi9p/K15_Ancients.png

    PCA (it makes sense and is in agreement with PCAs from scientific papers, but it seems that WHG samples plot too closely to BA Europe, and EEF plot too far away from BA Europe - why is it the case?):

    https://s18.postimg.org/vqby2v107/pca.png

    Biplot ("Atlantic" was present in Anatolian ENF, from Balkan HG?):

    https://s12.postimg.org/4akwgyj5n/biplot.jpg

    Which Gedmatch calculators would be best for Ancient samples?

    =============

    Only PC1 (here Kostenki14 plots almost exactly in the middle):

    https://s22.postimg.org/f5a7hote7/pc1.png

    In PC1 (40% of total variance), "Atlantic" is almost unimportant:

    https://s9.postimg.org/msjsejx5p/loadings.jpg

    Only in PC2 (21% of total variance) "Atlantic" has importance.

    Mds scatter plot: https://s22.postimg.org/wiwo09yqn/mds.png

    Does this tree of hierarchical clustering make sense?:

    https://s22.postimg.org/3mdiv9lrj/tree.png
    Last edited by Tomenable; 09-29-2016 at 01:50 PM.

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  11. #16
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    https://s22.postimg.org/f5a7hote7/pc1.png

    Interesting positions for Vestonice and Goyet, significantly closer to basal rich groups than WHG/ANE. This is not the first time that I saw Goyet and Vestonice behave like they were basal shifted. Natufians even prefer Vestonice over Villabruna with NMonte, and Vestonice shows up as Natufians+ANE
    (distance=0.070
    Vestonice16
    "Israel_Natufian" 52.35
    "AG3-MA1" 46.1
    "Papuan" 1.55).
    It would be interesting to try some Dstats like: Mbuti Villabruna Ust_Ishim Natufians; Mbuti Vestonice Ust_Ishim Natufians; Mbuti Goyet Ust_Ishim Natufians; Mbuti Vestonice Iran_Neo Natufians; Mbuti Villabruna Iran_Neo Natufians; Mbuti Goyet Iran_Neo Natufians; Or something that could check if WHG or UP Europe are a better fit for the west eurasian in natufians.

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  15. #18
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    With descriptions (IMO, looks fine & makes sense, even if WHG are a bit too close to Bronze Europe):

    Interestingly, Paleolithic El Miron plots in the same area as MLBA Europe, but it must be coincidence:

    http://s16.postimg.org/d5v0tx1et/PCA_described.png



    ==================

    Edit:

    If we add some modern Non-Sardinian Europeans to this PCA, I guess they will plot in this area:

    http://s9.postimg.org/rkmjd7cr3/Europeans.png

    Last edited by Tomenable; 09-29-2016 at 05:05 PM.

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  17. #19
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    Chalcolithic Armenian (I1631 from Areni-1, dated to 4250-4050 BCE) in HarappaWorld:

    Population
    S-Indian 0.27
    Baloch 17.64
    Caucasian 41.35
    NE-Euro 20.25
    SE-Asian -
    Siberian -
    NE-Asian -
    Papuan -
    American 0.55
    Beringian -
    Mediterranean 11.12
    SW-Asian 8.81
    San -
    E-African -
    Pygmy -
    W-African -

    That sample is from Areni-1, a lot of European admixture already in the Copper Age.

    Another Areni-1 Armenian had a typically Mesolithic European mtDNA haplogroup U4:



    Here are characteristic Mesolithic Euro mtDNA haplos: U8a, U8c, U5b, U5a (U5a1 + U5a2), U4 and U2.

    U5a1, U4, U2e, U5b2a1a1 were most common in East Europe. U5b, U5a2, U8a, U8c were more western.

    ============================

    Bronze Age Steppe had a mixture of Eastern European Mesolithic and other mtDNA haplos.

    From Eastern European hunters they had mostly: U5a1, U4, U2e, U2d2 and U5b2a1a1.

    They also had (most certainly from other groups) for example the following mtDNA:

    K1b, T1a, T2a1, T2c1, H6a1, H5, H2, H13, J1b, J2b1, I3, W6, W3a1a, X2b, N1a1, R1, C4a3

    ==================

    Yamnaya/Afanasievo/Poltavka/Catacomb samples:

    Gedmatch kit / culture and sample:

    M828815 / Yamnaya-RISE552
    M655536 / Yamnaya-I0231
    M343758 / Yamnaya-I0443
    F999968 / Yamnaya-RISE548
    F999942 / Afanasievo-RISE509
    M828784 / Afanasievo-RISE511
    M766878 / Poltavka-I0440
    F999946 / Catacomb-RISE552

    If you check them with HarappaWorld:

    Proportion of NE_Euro to Mediterranean admixture is about 2:1 for all these samples.

    So if Armenian Chalcolithic scores 20 NE_Euro + 10 Med, it could all be from Yamnaya.

    And Amerindian suggests some ANE (which could also be from Yamnaya).

    ==================

    Middle-Late Bronze Age Steppe samples:

    Gedmatch kit / culture and sample:

    M690970 / Sintashta-RISE386
    M277797 / Sintashta-RISE395
    M608028 / Andronovo-RISE505
    F999947 / Andronovo-RISE500
    F999961 / Andronovo-RISE503
    M472767 / Srubnaya-I0232
    M217196 / Srubnaya-I0430
    Last edited by Tomenable; 09-29-2016 at 10:00 PM.

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  19. #20
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    That PCA looks similar to PCAs from Lazaridis (which shows that this calculator works well with ancients):

    https://s32.postimg.org/qi9jt7u0z/wykres_PCA.png



    http://www.nature.com/nature/journal...re13673-f2.jpg


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