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Thread: Ancient I-M253 samples list

  1. #691
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    Quote Originally Posted by JonikW View Post
    Thanks very much for that. I always value your opinion, as you know, so do you have a further take on this sample? He seems to have a lot of valid markers, so why is the pretty uninformative I-L157.1 highlighted here and why might he have been excluded from the main study if that's actually the case?
    I don't see his sample among the BAM files at ENA, so there's no raw data for me to verify any of these SNPs (or any other I1-related SNPs). The description of I-L157.1 is as you say pretty uninfomative - it's a bit like saying I1 or I-M253, although I'm not sure why they called out L157 specifically (positive result for that one, and that's what they're using to define I1?). But without the BAM file to check corroborating SNPs on the I1 level, can't really say anything to confirm or disprove anything to do with this sample.

    As JMcB says above in #684, I'm struggling to find any mention of sample GOX287 in the paper, supplementary information or spreadsheets outside of a single mention in Table S5-2. Might just be same as him in that my eyes are tired and better to try again tomorrow.
    Last edited by deadly77; 05-28-2020 at 11:35 AM. Reason: Typo: L157.1 rather than L257.1
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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  3. #692
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    I think there might be two datasets in this paper, that were analyzed differently. Paper says "we genetically analyzed 243 unique individuals sampled from 54 different archeological sites, enriching for both complete mitochondrial genomes and a panel of 120 nuclear single-nucleotide polymorphisms (SNPs) including Y-chromosome SNPs, as well as a partially overlapping dataset of 58 low-coverage genomes" - so the 58 samples had what's equivalent to a low read-depth WGS, and the majority of 243 samples had the equivalent of a chip test which covered a few designated SNPs (autosomal and Y - but like say a 23andme test) and a full mitochondrial sequence. Perhaps this is why the majority of samples don't have a BAM file - only 58 of them do (which matches the numbers at ENA).
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    For samples which weren't shotgun sequenced they captured 47 regions on Y-chromosome totaling 4715 base pairs. I don't know how many phylogenetically relevant SNPs are in those regions in total, but in table S5-1 it can be seen that sample with largest number of valid SNPs (1360) is BOU11, but most of the rest have bellow 500.

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    Quote Originally Posted by deadly77 View Post
    I'd interpret this sample as being negative for the SNPs listed in the brackets by the nature of the x in front of all of these. Also, several of these are mutually exclusive - for example S1954, A196 and Y7198 are all on different branches of the I-Z140 group and can't allbe positive without conflicting each other.

    Compare with BES1248 in Table S5-2, listed as I-FGC9452* (xCTS6364, Z4727, S1289, etc...) checked a few of these in brackets and all negative for BES1248.

    I couldn't find FGC9452 on the YFull or FTDNA trees, but it is on the ISOGG tree on the I1 branch level (ie, not subclade) and it's at ChrY position (Hg38):10112707 close to the centromere.

    It is a bizarre designation. Youíre correct that I-FGC9452 is not on the Ftdna or YFull Haplotree. Itís simply listed as I1~ on the Isogg tree. What does the ~ even mean?
    I-DF29: ool009 Skane, Sweden 1930-1750 BCE

    Z58, Z59, Z2041, Z2040, Z382, FGC24333

    S26361: VK532 Zealand, Denmark 200-375 CE

    S16414, FGC24354, FGC24357, FGC24356, S10350

    FGC75802/BY19383: VK446 Funen, Denmark 800-1050 CE

    Y125947, S21197, BY149414, BY188003, BY188570

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    Quote Originally Posted by Pribislav View Post
    For samples which weren't shotgun sequenced they captured 47 regions on Y-chromosome totaling 4715 base pairs. I don't know how many phylogenetically relevant SNPs are in those regions in total, but in table S5-1 it can be seen that sample with largest number of valid SNPs (1360) is BOU11, but most of the rest have bellow 500.
    Interesting. In the case of GOX287 though, he was shotgun sequenced and has 5,653 valid SNPs.
    Living DNA's former Cautious mode:
    Wales-related ancestry: 86.8%
    Cornwall: 8%
    North England-related ancestry: 5.2%
    Y line: Peak District, England. Big Y match: Scania, Sweden; TMRCA 1,250 ybp (YFull);
    mtDNA: traces to Glamorgan, Wales
    Mother's Y: traces to Llanvair Discoed, Wales

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    Just trying to catch up on all this here!

    Wow! This is rather big stuff for I1. I thought BES1248 would be from somewhere in the north of France. I'm quite surprised, especially given his Z58 grouping. I wonder what this might mean for I-Y7198 lineages.

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    Quote Originally Posted by spruithean View Post
    Just trying to catch up on all this here!

    Wow! This is rather big stuff for I1. I thought BES1248 would be from somewhere in the north of France. I'm quite surprised, especially given his Z58 grouping. I wonder what this might mean for I-Y7198 lineages.

    Judging from his autosomal readings, I suspect he was from the North and ended up in the South. Unfortunately, his subclade appears to be in doubt at this point, too.

    https://anthrogenica.com/showthread....l=1#post666635


    I’m curious about these two early samples:

    FAD9 — I-A11354 — https://www.yfull.com/tree/I-A11341/

    An Early Bronze Age Z140 sample (1893-1700 BC) in Southern France.

    &

    Cx161 — FGC3466 — https://www.yfull.com/tree/I-S5619/

    An Middle Neolithic sample (4314-4052 BC) also in Occitanie.


    These are pretty early, I hope they check out.


    Hopefully, Deadly will get his hands on their Bam files in the near future.
    Last edited by JMcB; 05-28-2020 at 03:50 AM.
    Paper Trail: 42.25% English, 31.25% Scottish, 12.5% Irish, 6.25% German, 6.25% Italian & 1.5% French. Or: 86% British Isles, 6.25% German, 6.25% Italian & 1.5% French.
    LDNA(c): 86.3% British Isles (48.6% English, 37.7% Scottish & Irish), 7.8% NW Germanic, 5.9% Europe South (Aegean 3.4%, Tuscany 1.3%, Sardinia 1.1%)
    BigY 700: I1-Z140 >I-F2642 >Y1966 >Y3649 >A13241 >Y3647 >A13248 (circa 620 AD) >A13242/YSEQ (circa 765 AD) >FT80854 (circa 1650 AD).

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    Quote Originally Posted by mwauthy View Post
    It is a bizarre designation. You’re correct that I-FGC9452 is not on the Ftdna or YFull Haplotree. It’s simply listed as I1~ on the Isogg tree. What does the ~ even mean?
    It is a bit bizarre, but it's not unique. The Anglo-Saxon NO3423 from Martiniano et al Nat. Commun 2016 was listed as I1-S107, and there's usually many posts on the I-M253 facebook page from folks who have run data through the Morley haplogroup predictor and got "I-L759" and they ask about it as a subclade. Both of these SNPs are in the block of >300 SNPs on the I1 branch before diversification but it essentially means I-M253 - ie, I1 without a defined subclade.

    Perhaps the authors didn't want to use the designation I-M253 unless the sample was actually positive for M253 the SNP itself. I checked position ChrY(hg19):15022707 and it's a no call in BES1248's BAM file. So perhaps they picked one of the phyloquivalent SNPs that he's positive for to use instead. So I-FGC9452 for BES1248 and and I-L127.1 for GOX287. But it actually just means I1 with no confirmed subclade.

    For what it's worth, I'm positive for FGC9452 (19C) and L127.1 (23G) as an I1 person.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    Quote Originally Posted by spruithean View Post
    Just trying to catch up on all this here!

    Wow! This is rather big stuff for I1. I thought BES1248 would be from somewhere in the north of France. I'm quite surprised, especially given his Z58 grouping. I wonder what this might mean for I-Y7198 lineages.
    I don't think there's enough evidence to confirm BES1248 in the I-Z58 group. He has a one read positive in his BAM file for S10350, but that's contradicted by a one read negative for S22349, which is a phyloequivalent SNP on the I-FGC24354 branch three steps up. Both of these can't be right and phylogenetically consistent with each other and BES1248 is no call for all other SNPs between I-S10350 back to the I1, including I-Z58 and I-DF29 branch. If there were more SNPs in this lineage that were positive or negative, that may swing it one way or another, but all no calls makes that decision more difficult.

    I think it's safer ground to categorize him as at the basic I1 level, where there's more corroborating evidence - 19 positive SNPs at the I1 level (20 if you include FGC9452) that are all in agreement with each other. I guess it's accuracy versus precision. I1 with no defined subclade is more accurate. I-S10350 (or Z58) is more precise but has a high possibility of not being very accurate based on the evidence available.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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    Quote Originally Posted by JMcB View Post
    Judging from his autosomal readings, I suspect he was from the North and ended up in the South. Unfortunately, his subclade appears to be in doubt at this point, too.

    https://anthrogenica.com/showthread....l=1#post666635


    I’m curious about these two early samples:

    FAD9 — I-A11354 — https://www.yfull.com/tree/I-A11341/

    An Early Bronze Age Z140 sample (1893-1700 BC) in Southern France.

    &

    Cx161 — FGC3466 — https://www.yfull.com/tree/I-S5619/

    An Middle Neolithic sample (4314-4052 BC) also in Occitanie.


    These are pretty early, I hope they check out.


    Hopefully, Deadly will get his hands on their Bam files in the near future.
    Not sure BAM files will be available for these ones, given the method of DNA analysis used, although that depends on the details. If it's a genotyped chip test - like a custom version of the arrays used by 23andme, Ancestry, etc. then I think it's unlikely that there will be a BAM file and we'll only get a BAM file for the 58 low coverage shotgun sequenced samples such as BES1248. If it's a SNP capture similar to what the researchers in the Avar burials used, we may get a BAM with a lot of holes in it. Or if the SNPs results came from a Sanger (similar to a YSEQ single SNP test) then perhaps that could be assembled into a BAM file. The latter two cases mean we're unlikely to get anything "new" from the data, but perhaps can confirm the calls rather than taking them on trust from a spreadsheet.

    If not a BAM file (in the case of a genotyped chip test) then hopefully we can look at some of the other calls and see if the final ones are phylogenetically consistent. My AncestryDNA test has positive SNPs for Z1842 (haplogroup J), CTS616 (haplogroup I2), M307/P203 (haplogroup O) but those single SNPs alone don't define me as any of those haplogroups. Can verify these are false positives by looking at upstream negatives - for example, I'm negative for L134/PF4539, M304, L60/S6, M267, Z2215, Z1828 in haplogroup J which contradict the positive resut for Z1842. So if we could get something similar for FAD9 or Cx161 then we can be a bit more confident.
    Haplogroup I1 Ancient DNA Samples Map: Hidden Content

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