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Thread: First ancient DNA from mainland Finland reveals origins of Siberian ancestry in regio

  1. #101
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  2. #102
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    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

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     randwulf (12-04-2018)

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    The previous admixture run was a quick and dirty job. Here is a more cautious one, nearly the same spreadsheet but filtered through --geno (0.4: kept only the SNPs present in at least 60% of the individuals): 681441 variants removed due to missing genotype data (--geno). 469198 variants and 87 people pass filters and QC.

    stackedchart in jpg and pdf:
    stackedgeno6.jpg
    stackedgeno6.pdf

    The files are of course available.

    edit: ADMIXTURE is likely not the best tool for this sort of study, to say the least. I'm in particular puzzled by the Levanluhta. I've published these results just because they were on my disk, but honnestly I'm very disapointed, as most often with admixture.
    Last edited by anglesqueville; 12-04-2018 at 03:36 PM.
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

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     Kristiina (12-04-2018)

  6. #104
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    I would like to be sure what those ...enets:GS000 samples are? I presume they are Nenets. How about the samples after that, where are they from (between enets and DA236)?

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    Quote Originally Posted by Kristiina View Post
    I would like to be sure what those ...enets:GS000 samples are? I presume they are Nenets. How about the samples after that, where are they from (between enets and DA236)?
    Hum, yes the labels have been trimmed. They are Nenets of course (forest_N and tundra_N. I seem to remember that they come from EGDP). Here is the whole list:

    BOO001 Bolshoy_Oleni_Ostrov
    BOO002 Bolshoy_Oleni_Ostrov
    BOO003 Bolshoy_Oleni_Ostrov
    BOO004 Bolshoy_Oleni_Ostrov
    BOO005 Bolshoy_Oleni_Ostrov
    BOO006 Bolshoy_Oleni_Ostrov
    CHV001 Chalmny-Varre
    CHV002 Chalmny-Varre
    JK1963 Levanluhta_IA
    JK1967 Levanluhta_IA
    JK1968 Levanluhta_IA
    JK1970 Levanluhta_IA
    JK2065 Levanluhta_IA_o
    JK2066 Levanluhta_IA
    JK2067 Levanluhta_IA
    Saami001 Saami
    I0432 Samara_Eneolithic
    I0434 Samara_Eneolithic
    I0433 Samara_Eneolithic
    I0122 Samara_Eneolithic
    I0124 Samara_HG
    I4595 Latvia_HG
    I4596 Latvia_HG
    I4630 Latvia_HG
    I4632 Latvia_HG
    Donkalnis4 Baltic_HG
    Donkalnis6 Narva_Lithuania
    Donkalnis7 Narva_Lithuania
    Gyvakarai1 CWC_Baltic_early
    Kivisaare3 Narva_Estonia
    Kivutkalns153 Baltic_BA
    Kivutkalns164 Baltic_BA
    Kivutkalns194 Baltic_BA
    Kivutkalns19 Baltic_BA
    Kivutkalns207 Baltic_BA
    Kivutkalns209 Baltic_BA
    Kivutkalns215 Baltic_BA
    Kivutkalns222 Baltic_BA
    Kivutkalns25 Baltic_BA
    Kivutkalns42 Baltic_BA
    Kretuonas1 Narva_Lithuania
    Kretuonas2 Narva_Lithuania
    Kretuonas4 Narva_Lithuania
    Kretuonas5 Narva_Lithuania
    Kunila2_merged CWC_Baltic
    MotalaAA SHG
    Olsund Battle-Axe
    Plinkaigalis241 CWC_Baltic
    Plinkaigalis242 CWC_Baltic_early
    Popovo2 EHG
    Saxtorp5164 Sweden_EN
    Spiginas1 Narva_Lithuania
    Spiginas2 CWC_Baltic
    Spiginas4 Baltic_HG
    Tamula1 Combed_Ceramic
    Tamula3 Combed_Ceramic
    Turlojiske1 Baltic_BA
    Turlojiske1932 Baltic_BA
    Turlojiske3 Baltic_BA
    Turlojiske5 Baltic_BA
    UzOO77 EHG
    Veibri4 Narva_Estonia
    GS000013714-ASM Forest-Nenets
    GS000014337-ASM Forest-Nenets
    GS000015879-ASM Forest-Nenets
    GS000016161-ASM Tundra-Nenets
    GS000016162-ASM Tundra-Nenets
    GS000016163-ASM Tundra-Nenets
    GS000016894-ASM Finnish
    GS000016895-ASM Finnish
    GS000018756-ASM Finnish
    GS000035024-ASM Saami
    GS000035025-ASM Saami
    GS000035026-ASM Saami
    DA236 Anc_Finn
    DA234 Anc_Saami
    DA237 Anc_Saami
    DA238 Anc_Saami
    DA171 Baltic_IA
    BOT14 Botai
    BOT15 Botai
    BOT2016 Botai
    Sidelkino EHG
    By the way, I checked and the genotype rate of Levanluhta individuals is really very low. No wonder their admixture results are so strange
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

  8. #106
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    Thank you! Very interesting!

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     anglesqueville (12-04-2018)

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    Quote Originally Posted by Kristiina View Post
    Thank you! Very interesting!
    Kristiina, I read the answers to your message on Eurogenes and I agree with David. As I said, the genotype rate (not to mention the quality) of some samples, including Levanluhta, is really scary. Consider this as a risky, unconvincing test. We have to wait for better samples, and for my part, I'll continue to wait especially for (or dream of) pre-saami samples because imo the nature of the palaeo-laplandic populations is even much more mysterious than what happened with the bronze and iron ages.
    En North alom, de North venom
    En North fum naiz, en North manom

    (Roman de Rou, Wace, 1160-1170)

  11. #108
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    Ok, it is indeed a pity that the Levšluhta samples are so poor. Moreover, it was a weird burial because nearly all buried are females.

    However, we definitely need analyses of the type above to be able to understand the Saami ethnogenesis. I think that it will be much more interesting than the ethnogenesis of Finns.

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     anglesqueville (12-05-2018)

  13. #109
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    Quote Originally Posted by Kristiina View Post
    Ok, it is indeed a pity that the Levšluhta samples are so poor. Moreover, it was a weird burial because nearly all buried are females.

    However, we definitely need analyses of the type above to be able to understand the Saami ethnogenesis. I think that it will be much more interesting than the ethnogenesis of Finns.
    The quality overall is just fine for most analyses.

    It's just that some of the individuals can't be run in ADMIXTURE tests with few samples because they don't have enough markers and so they'll skew the analysis. But an ADMIXTURE run with a couple thousand of present-day samples would produce accurate results for them.

    Can't believe though that you took those results seriously. Or maybe I can...

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