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Thread: A dynamic 6,000-year genetic history of Eurasia’s Eastern Steppe

  1. #51
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    The team has collected 124 samples, they have identified both yDNA and mtDNA haplogroups and made a good-quality autosomal analysis of the samples with great figures and charts. If there are some errors in the archaelogical or geographical description of a couple of samples, it is not very important. They can be easily corrected in the final publication. I very much respect the work of this team. They give us a unique opportunity to understand the population history of the eastern steppe.

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  3. #52
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    Quote Originally Posted by Kristiina View Post
    The team has collected 124 samples, they have identified both yDNA and mtDNA haplogroups and made a good-quality autosomal analysis of the samples with great figures and charts. If there are some errors in the archaelogical or geographical description of a couple of samples, it is not very important. They can be easily corrected in the final publication. I very much respect the work of this team. They give us a unique opportunity to understand the population history of the eastern steppe.
    One cannot tell if a post is meant to gaslight; without any direct examples.


    Peer review is the evaluation of work by one or more people with similar competences as the producers of the work (peers). It functions as a form of self-regulation by qualified members of a profession within the relevant field. Peer review methods are used to maintain quality standards, improve performance, and provide credibility. In academia, scholarly peer review is often used to determine an academic paper's suitability for publication. Peer review can be categorized by the type of activity and by the field or profession in which the activity occurs, e.g., medical peer review.
    What? How did this get by without an objective peer review?

    good-quality autosomal analysis
    Please remember this when it comes to explaining Afanasievo sample R1b-L52-- 16222
    incredibly dated to 3316-2918BC+ and the Western Dutch-Corded Ware Bell Beakers R1b-L52 samples. Hopefully some interested genetic Blogger will devout a blog to the interesting find of Afansievo R1b- L52+ in Mongolia.


    A very interesting point is that there is R1b1a1a2a2-Z2103 both in Afanasievo and Chemurchek, but they are autosomally completely different. Chemurchek harbours Baikal EBA and BMAC ancestry and their language could indeed be related to BMAC languages. R1b only reappers with Xiongnus, but it is probably R1b2-PH155.
    FYI
    Afansievo-Chemurchek-Jungar basin- share the same nonrecombinant phylogeny M269+L23+ markers with Afanasievo speaking tribes 16222 R1b-L52 and all non R1a Corded Ware/Western European Bell Beakers.

    Jungar basin has been proposed by some as the dividing line between Tocharian A branch and Tocharian B branch

    There was a time not all that long ago[let's call it the age of tomatoes-peer reviewed-no names mentioned] people were drawing lines of R1b- M269 from the Middle East, and R1b-L52 in Northern Africa entering Spain Bell Beakers.
    Last edited by Silesian; 03-31-2020 at 10:29 AM.
    Time has come stop using Yamnaya L23 and Z2109 as shareware samples to reconstruct -L151+ R1a history .

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  5. #53
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    On the topic of mislabeled samples, I noticed in the reichlab v42.4 compilation I7760 and I7781 are given the same information as they were in the original Flegontov et al. publication.
    I strongly suspect the information for these two samples has been swapped. Here is from my correspondence with Dr. Flegontov on the matter...
    The sample provider who shared the Ekven and Uelen samples is not a reliable one, so mixups are unfortunately possible. We've already corrected two such cases while preparing the paper. I will try to inquire and understand what happened.
    Unfortunately I have heard nothing back, then again I haven't inquired further.
    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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  7. #54
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    Sample I14460/I14461 from the Sirak paper (not the same sample as FNO001 from the new Jeong paper):

    I14460/I14461; 6000-3000 BC; Fofonovo, Buryatia, Russia; Fofonovo_Eneolithic; N1a1-TAT>F1419>Y24317>pre-B187

    B187 level:

    Y23777+ A>G (2 reads)
    Y23751+ C>T (3 reads)
    Y24330+ C>A (4 reads)
    Y24332+ C>T (1 read)
    Y24269+ G>C (4 reads)
    Y24270+ G>T (5 reads)
    Y24307+ G>A (1 read)
    Y24337+ G>T (1 read)
    Y24347+ G>A (2 reads)
    Y24326+ T>G (1 read)
    Y23780+ T>C (1 read)
    Y24297- G>A (9 reads)
    Y24354- G>A (4 reads)
    Y24343- T>C (1 read)
    Y24279? G>A (9 derived, 22 ancestral reads)

    This is the second ancient sample from the Baikal region that belongs to this rare subclade:

    Quote Originally Posted by Pribislav View Post
    DA345, ~3000 BC, Ust'-Ida, Isakovo Late Neolithic, N1a1-TAT>F1419>Y24317>pre-B187 (32/73 SNPs covered: 15 derived, 17 ancestral)

    So, DA345 was partial B187 (~45-50%). This subclade is confined almost exclusively to Southern Siberia today, with highest percentages among Khakas (~20%), Shors (~15%) and Tuvans (~5%).
    Last edited by Pribislav; 04-01-2020 at 06:59 PM.

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    Since there is not much factual peer reviewing,
    just want to correct my post #53 - Tarim basin,Turfan Basin, Jungar basin

    FYI
    Afansievo-Chemurchek-Jungar basin- share the same nonrecombinant phylogeny M269+L23+ markers with Afanasievo speaking tribes 16222 R1b-L52 and all non R1a Corded Ware/Western European Bell Beakers.

    Jungar basin has been proposed by some as the dividing line between Tocharian A branch and Tocharian B branch

    There was a time not all that long ago[let's call it the age of tomatoes-peer reviewed-no names mentioned] people were drawing lines of R1b- M269 from the Middle East, and R1b-L52 in Northern Africa entering Spain Bell Beakers.[
    Jungar basin-
    Dzungaria is home to a semi-desert steppe ecoregion known as the Dzungarian Basin semi-desert. ....The basin was one of the last habitats of Przewalski's horse (Equus przewalskii), also known as Dzungarian horse
    The Dzungarian Gate is a geographically and historically significant mountain pass between China and Central Asia.[1]

    Jiaohe (Nearer Jushi)-Tocharian A [toward Turfan Basin?]
    Agni (Karashahr, Yanqi)-Tocharian A and B
    Kucha-Tocharian B

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  11. #56
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    Two more interesting samples from the Sirak paper:

    I11954/I11955; 3500-3000 BC; Glăvăneşti, Romania; Late Cucuteni–Trypillia culture; R1a-Z93 (xZ94,YP5578,YP1451,Y34351,Y39884,YP1506,YP5321)

    Z93 level: V3664/S4582/AM01870/Z2479/M746+ C>A (5 reads)

    Z93>Z94 level: F3568/Z95- C>T (3 reads)

    I18130/I18131; 1400-1200 BC; Olmo di Nogara, Italy; Terramare_MLBA; R1b-L51>(pre?)Z2118 (xZ4416,Y5141,Y5617,FGC24138,PF7592)

    Z2118 level: Z2119/CTS7153+ G>C (3 reads); Z2114- C>T (1 read)

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  13. #57
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    Quote Originally Posted by Pribislav View Post
    Two more interesting samples from the Sirak paper:

    I11954/I11955; 3500-3000 BC; Glăvăneşti, Romania; Late Cucuteni–Trypillia culture; R1a-Z93 (xZ94,YP5578,YP1451,Y34351,Y39884,YP1506,YP5321)

    Z93 level: V3664/S4582/AM01870/Z2479/M746+ C>A (5 reads)

    Z93>Z94 level: F3568/Z95- C>T (3 reads)
    That's got to reflect infiltration by steppe pastoralists into CT, which Gimbutas mentioned.

    Quote Originally Posted by Pribislav View Post
    I18130/I18131; 1400-1200 BC; Olmo di Nogara, Italy; Terramare_MLBA; R1b-L51>(pre?)Z2118 (xZ4416,Y5141,Y5617,FGC24138,PF7592)

    Z2118 level: Z2119/CTS7153+ G>C (3 reads); Z2114- C>T (1 read)
    I read that some scholars view Terramare as the early Ligurians, while at least one scholar thought they were Pelasgians.

    Don't see any reason to think L51 could be Pelasgian, so Ligurian seems more likely in this context.

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    Quote Originally Posted by Pribislav View Post
    Two more interesting samples from the Sirak paper:

    I11954/I11955; 3500-3000 BC; Glăvăneşti, Romania; Late Cucuteni–Trypillia culture; R1a-Z93 (xZ94,YP5578,YP1451,Y34351,Y39884,YP1506,YP5321)

    Z93 level: V3664/S4582/AM01870/Z2479/M746+ C>A (5 reads)

    Z93>Z94 level: F3568/Z95- C>T (3 reads)
    ...
    Pribislav,
    Anyway to find out how many 'private' SNPs downstream of Z93 this sample has?
    That would help estimate how close to ancestral Z93 this sample is.

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  17. #59
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    Quote Originally Posted by parasar View Post
    Pribislav,
    Anyway to find out how many 'private' SNPs downstream of Z93 this sample has?
    That would help estimate how close to ancestral Z93 this sample is.
    Even novel SNPs found by YFull are added to the YBrowse tree (at least with my sample), so in theory you could grab an up-to-date .vcf.gz file from YBrowse containing the SNPs on their database, and run bcftools isec with a .vcf.gz file generated from the BAM itself (I use bcftools mpileup) and the YBrowse.vcf.gz file and then see what SNPs the sample has that are not present in the YBrowse.vcf.gz file. In reality, many of the SNPs highlighted in the sample vcf.gz are likely to be mixed reads and/or have a mapping quality of 0 so that is something to bear in mind.

    If you can provide a link to these BAMs, I can do this for you.
    YFull: YF72440 (FTDNA - IN41220)

    Ancestral Haplos (Punjabi Jatt):
    * Father: R2-SK2142 > A26339 - M5a1a
    * Maternal Uncle: R1b-Z2109 > Y84821 - U7a3a
    * MGMs F (?): L-M22 > M357 - ?
    * PGMs F (?): Q-F1096 > F4747 - ?
    * MGMs MGF (?): R1a-Z93 > Y7 - ?

    Friends Haplos:
    * North Moroccan Berber: E-M35 > M81 - R0
    * Han Chinese: O-M117 > F1531 - M7e
    * Gujarati Lohana (?): T-Y11151 > Y13290 - R30b1

    Hidden Content

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  19. #60
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    Quote Originally Posted by parasar View Post
    Pribislav,
    Anyway to find out how many 'private' SNPs downstream of Z93 this sample has?
    That would help estimate how close to ancestral Z93 this sample is.
    There's really no use checking for novel variants when the samples are 1240K sequenced, since the libraries are being enriched only for already known SNPs. Also, initial shallow shotgun sequencing used to estimate the proportion of endogenous DNA just can't produce enough useful data.

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