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Thread: AncIBD: IBD in ancient DNA

  1. 10-03-23, 12:55 #1
    Jovialis
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    AncIBD: IBD in ancient DNA

    https://twitter.com/HaraldRingbauer/...412672/photo/1

    the paper link seems to be broken, but here is a tweet from the author.
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  2. 10-03-23, 12:58 #2
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    Will this bring on the end of hypothetical modeling, for more precise analysis? That would be pretty cool.
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  3. 10-03-23, 13:00 #3
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    "We reveal that Corded Ware groups in Europe 4.5kya, the first with a high fraction of Steppe ancestry, share long IBD links with Yamnaya Steppe herders - indicating a very recent connection. Also, CW are linked to GAC farmers from East Europe with no Steppe ancestry yet. (4/5)"
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  4. 10-03-23, 17:43 #4
    Kuivamaa
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    So the thesis that CW is largely a byproduct of yamnaya males getting farmer women is getting even more robust, regardless of the perceived difference in y haplos between CWC and yamnaya.
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  5. 10-03-23, 17:59 #5
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    Could this tool be used to settle the dispute about the Southern Arc once and for all? That would really be something.
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  6. 10-03-23, 18:13 #6
    Salento
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    Quote Originally Posted by Jovialis View Post
    https://twitter.com/HaraldRingbauer/...412672/photo/1

    the paper link seems to be broken, but here is a tweet from the author.
    … link to pdf :

    https://www.biorxiv.org/content/10.1...671v1.full.pdf
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  7. 10-03-23, 18:24 #7
    Jovialis
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    Thanks Salento:

    Moreover, there are several intriguing observations regarding individuals associatedwith the Corded Ware culture, who are the earliest Central and Northern Europeans tocarry high amounts of Steppe-like ancestry. Previous aDNA research has shown them tobe a genetic mix of previous Final Neolithic farmer cultures as well as Steppe-like ancestry[Haak et al., 2015, Allentoft et al., 2015, Papac et al., 2021]. Using IBD, we find that individuals from diverse Corded Ware cultural groups, including from Sweden (associatedwith the Battle Axe culture), Russia (Fatyanovo), and East/Central Europe share highamounts of long IBD with each other, and also have IBD sharing up to 20 cM with various Yamnaya groups (Fig. 5, Fig. E2). Importantly, we find a distinctive IBD signal withthe so-called Globular Amphora culture, in particular from Poland and Ukraine, whowere Copper Age farmers not yet carrying Steppe-like ancestry [Mathieson et al., 2018,Schroeder et al., 2019]. This IBD link to Globular Amphora appears for all Corded Waregroups in our analysis, including from as far away as Scandinavia and Russia (Fig. 5),which indicates that individuals related to Globular Amphora contexts from Eastern Europe must have had a major demographic impact early on in the genetic admixtures giving rise to various Corded Ware groups.
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  8. 10-03-23, 21:21 #8
    Anfänger
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    Quote Originally Posted by Jovialis View Post
    Could this tool be used to settle the dispute about the Southern Arc once and for all? That would really be something.
    Thanks for sharing Jovialis. I hope it does and upcoming papers will use this tool to analyze the two waves Lazaridis proposed. We could get precise modeling about the second wave if it is from Meshoko/Maikop or from European farmers. I think for the first wave there aren’t enough published samples yet. Let’s see what the future will bring.
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  9. 15-03-23, 14:40 #9
    Jovialis
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    Quote Originally Posted by Anfänger View Post
    Thanks for sharing Jovialis. I hope it does and upcoming papers will use this tool to analyze the two waves Lazaridis proposed. We could get precise modeling about the second wave if it is from Meshoko/Maikop or from European farmers. I think for the first wave there aren’t enough published samples yet. Let’s see what the future will bring.
    I believe I saw Haak on Twitter refer to this pre-print as "the future".

    I think this will probably be the biggest revolution in the field since scientists discovered they could extract aDNA from the petrous bone.
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  10. 16-03-23, 07:40 #10
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    IBD: R1, R437, R850, R474, VK537 (Foggia), and R57 ... Supplementary Spreadsheet:

    https://www.biorxiv.org/content/bior...?download=true

    iid1 iid2 max_IBD sum_IBD>8 n_IBD>8 sum_IBD>12 n_IBD>12 sum_IBD>16 n_IBD>16 sum_IBD>20 n_IBD>20
    R1









    I14690 R1.SG 17.201301 50.46230145 4 32.566302 2 17.201301 1 0 0
    I13777 R1.SG 11.1588 11.15880013 1 0 0 0 0 0 0
    I10391 R1.SG 9.0941072 9.094107151 1 0 0 0 0 0 0
    HOP001 R1.SG 9.0911031 9.091103077 1 0 0 0 0 0 0
    I2457 R1.SG 9.0579033 9.05790329 1 0 0 0 0 0 0
    RK4002 R1.SG 8.7428093 8.742809296 1 0 0 0 0 0 0
    VK348_noUDG.SG R1.SG 8.7193966 8.719396591 1 0 0 0 0 0 0
    I6764.SG R1.SG 8.5376978 8.537697792 1 0 0 0 0 0 0
    R3659.SG R1.SG 8.2758009 8.275800943 1 0 0 0 0 0 0
    MIB052 R1.SG 8.2211003 8.221100271 1 0 0 0 0 0 0
    I8371 R1.SG 8.1791937 8.179193735 1 0 0 0 0 0 0
    R11105.SG R1.SG 8.1541002 8.15410018 1 0 0 0 0 0 0











    R437









    VK313_noUDG.SG R437.SG 11.595905 11.59590483 1 0 0 0 0 0 0
    R10340.SG R437.SG 9.9575043 9.957504272 1 0 0 0 0 0 0
    SUC001 R437.SG 8.1436992 8.143699169 1 0 0 0 0 0 0
    VLI071 R437.SG 8.0231905 8.023190498 1 0 0 0 0 0 0











    R850









    R850.SG I3917_noUDG 12.2812 12.28120029 1 12.2812 1 0 0 0 0
    R850.SG R1543.SG 9.6928954 9.692895412 1 0 0 0 0 0 0
    R850.SG I10045 9.2979968 9.297996759 1 0 0 0 0 0 0
    R850.SG GRG008 8.0380991 8.03809911 1 0
    		0 0 0 0











    R474









    R474.SG I18745 12.547201 12.54720092 1 12.547201 1 0 0 0 0
    R474.SG AITI_72 10.701099 10.70109904 1 0 0 0 0 0 0
    R474.SG LBR002 9.0368032 9.036803246 1 0 0 0 0 0 0
    R474.SG AITI_78 8.9351982 8.935198188 1 0 0 0 0 0 0
    R474.SG I19869 8.4379017 8.437901735 1 0 0 0 0 0 0
    R474.SG I0443 8.4369004 8.436900377 1 0 0 0 0 0 0
    R474.SG KO1006 8.2661033 8.266103268 1 0 0 0 0 0 0
    R474.SG I13792 8.1110001 8.111000061 1 0 0 0 0 0 0
    R474.SG I10063 8.0649018 8.064901829 1 0 0 0 0 0 0











    VK537 (Foggia)









    VK314_noUDG.SG VK537_noUDG.SG 10.155499 10.15549898 1 0 0 0 0 0 0
    VK537_noUDG.SG ROUQCC.SG 9.9086046 9.908604622 1 0 0 0 0 0 0
    VK369_noUDG.SG VK537_noUDG.SG 9.4323993 9.432399273 1 0 0 0 0 0 0
    VK312_noUDG.SG VK537_noUDG.SG 9.3397975 9.339797497 1 0 0 0 0 0 0
    VK537_noUDG.SG I10348 9.0422004 9.042200446 1 0 0 0 0 0 0
    VK537_noUDG.SG VK357_noUDG.SG 8.8852048 8.885204792 1 0 0 0 0 0 0
    VK460_noUDG.SG VK537_noUDG.SG 8.7768003 8.776800334 1 0 0 0 0 0 0
    VK69_noUDG.SG VK537_noUDG.SG 8.7054014 8.705401421 1 0 0 0 0 0 0
    ros005_renamed_noUDG.SG VK537_noUDG.SG 8.5605025 8.560502529 1 0 0 0 0 0 0
    VK175_noUDG.SG VK537_noUDG.SG 8.5051 8.505100012 1 0 0 0 0 0 0
    VK537_noUDG.SG I14831 8.4825993 8.482599258 1 0 0 0 0 0 0
    I7604 VK537_noUDG.SG 8.4707975 8.470797539 1 0 0 0 0 0 0
    VK340_noUDG.SG VK537_noUDG.SG 8.3926916 8.392691612 1 0 0 0 0 0 0
    VK537_noUDG.SG I2532 8.355099 8.355098963 1 0 0 0 0 0 0
    VK537_noUDG.SG PG2001 8.3406001 8.340600133 1 0 0 0 0 0 0
    VK338_noUDG.SG VK537_noUDG.SG 8.3378971 8.337897062 1 0 0 0 0 0 0
    RISE675_noUDG.SG VK537_noUDG.SG 8.2602024 8.260202408 1 0 0 0 0 0 0
    VK537_noUDG.SG VK528_noUDG.SG 8.2367986 8.236798644 1 0 0 0 0 0 0
    VK537_noUDG.SG I4887 8.1395 8.139500022 1 0 0 0 0 0 0
    PN107.SG VK537_noUDG.SG 8.0098987 8.009898663 1 0 0 0 0 0 0











    R57









    ETR013 R57.SG 9.5937014 9.593701363 1 0 0 0 0 0 0
    VK27_noUDG.SG R57.SG 8.5254014 8.525401354 1 0 0 0 0 0 0
    R57.SG R61.SG 8.2430959 8.243095875 1 0 0 0 0 0 0
    I4558 R57.SG 8.1179857 8.117985725 1 0 0 0 0 0 0
    VK432_noUDG.SG R57.SG 8.0532074 8.053207397 1 0 0 0 0 0 0
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  11. 16-03-23, 16:25 #11
    Salento
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    IBD: Villabruna (Italy_North_HG)

    iid1 iid2 max_IBD sum_IBD>8 n_IBD>8 sum_IBD>12 n_IBD>12 sum_IBD>16 n_IBD>16 sum_IBD>20 n_IBD>20
    I5241 Serbia_IronGates_Mesolithic Villabruna_noUDG 15.597904 15.597904 1 15.597904 1 0 0 0 0
    R11.SG Italy_Abruzzo_Mesolithic Villabruna_noUDG 13.3811 30.919194 3 13.3811 1 0 0 0 0
    I14168 Czech_C_Baalberge Villabruna_noUDG 12.038898 12.038898 1 12.038898 1 0 0 0 0
    Villabruna_noUDG I6767_noUDG.SG England_Mesolithic 10.627198 27.597391 3 0 0 0 0 0 0
    SB460A3_lib.SG Wales_Mesolithic Villabruna_noUDG 9.9814013 18.316896 2 0 0 0 0 0 0
    Villabruna_noUDG ROUQCC.SG France_LaClape_LN_EMBA 9.8937992 9.8937992 1 0 0 0 0 0 0
    RISE1159_noUDG.SG Poland_Koszyce_GlobularAmphora Villabruna_noUDG 9.7688079 9.7688079 1 0 0 0 0 0 0
    PN112.SG Ireland_EN_MN Villabruna_noUDG 9.6035004 9.6035004 1 0 0 0 0 0 0
    Spiginas4 Lithuania_Mesolithic Villabruna_noUDG 9.4880819 9.4880819 1 0 0 0 0 0 0
    SB573A_lib.SG Wales_N Villabruna_noUDG 9.4597936 9.4597936 1 0 0 0 0 0 0
    I5411 Romania_IronGates_Mesolithic Villabruna_noUDG 9.3948007 9.3948007 1 0 0 0 0 0 0
    KGH6.SG Ireland_Mesolithic Villabruna_noUDG 9.127003 17.148603 2 0 0 0 0 0 0
    Villabruna_noUDG R15.SG Italy_Abruzzo_Mesolithic 9.008801 17.396802 2 0 0 0 0 0 0
    Villabruna_noUDG R7.SG Italy_Abruzzo_Mesolithic 8.7661982 8.7661982 1 0 0 0 0 0 0
    Villabruna_noUDG I0843 Spain_HG 8.761096 8.761096 1 0 0 0 0 0 0
    Villabruna_noUDG Chan_noUDG.SG Spain_HG 8.3828986 8.3828986 1 0 0 0 0 0 0
    BDB001 Germany_Mesolithic Villabruna_noUDG 8.3537996 8.3537996 1 0 0 0 0 0 0
    BNL003 Czech_EBA_Unetice Villabruna_noUDG 8.1896901 8.1896901 1 0 0 0 0 0 0
    UZZ4446_noUDG Italy_Sicily_LateMesolithic_Castelnovian Villabruna_noUDG 8.1833005 8.1833005 1 0 0 0 0 0 0
    UZZ071_noUDG Italy_Sicily_LateMesolithic Villabruna_noUDG 8.1249952 8.1249952 1 0 0 0 0 0 0
    VK325_noUDG.SG Denmark_Viking Villabruna_noUDG 8.1164002 8.1164002 1 0 0 0 0 0 0
    I4916 Serbia_IronGates_Mesolithic Villabruna_noUDG 8.0947995 8.0947995 1 0 0 0 0 0 0
    VK312_noUDG.SG Denmark_Viking Villabruna_noUDG 8.0270946 8.0270946 1 0 0 0 0 0 0
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