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Thread: Y Chromosome Haplogroup assignments for ~2500 ancient samples

  1. #41
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    Quote Originally Posted by Nibelung View Post
    So the Yumin sample is N-TAT? Rad. Since 2014 they've found a few of their sites. Apparently the original (Yumin) they later determined to be the spare winter residence vs Simagou.
    According to the paper, Yumin is a female:

    Yumin – The Yumin archaeological site is located in Huade County, Ulanqab city, Inner Mongolia Autonomous Region of China. Yumin culture is the earliest Neolithic culture found in Inner Mongolia thus far. Radiocarbon analysis of charcoal samples associated with the remains of a house were dated to ~8,400 cal BP (62). We sequenced a single individual (M1) from this site, identified to be female, and she was directly radiocarbon dated to 8,415-8,335 cal BP.

    Yumin data.PNG

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  3. #42
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    Quote Originally Posted by Kristiina View Post
    According to the paper, Yumin is a female:

    Yumin – The Yumin archaeological site is located in Huade County, Ulanqab city, Inner Mongolia Autonomous Region of China. Yumin culture is the earliest Neolithic culture found in Inner Mongolia thus far. Radiocarbon analysis of charcoal samples associated with the remains of a house were dated to ~8,400 cal BP (62). We sequenced a single individual (M1) from this site, identified to be female, and she was directly radiocarbon dated to 8,415-8,335 cal BP.

    Yumin data.PNG
    That's what I thought. I'm sure the team can provide clarification, as if it really matters. Audiences dream. A sample couldn't be both real and some imaginary trans being.
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  5. #43
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    Quote Originally Posted by deadly77 View Post
    Are you sure about SZ20 Hungary_Langobard_lc I1 (post #8)? I haven't checked the BAM file myself but SZ20 is R1a1a1b2a2a in the Supplementary Data of the Amorim et al paper and I believe it's been checked by other folks on this forum to verify SNPs downstream of R-U106 (U106/S21>Z2265>Z381/S263).

    For I1282 Iberia_C I or I1a1a4a1a1b2 (post #9) this is unlikely to be I1. I'd previously been through the BAM file manually and there are 9 SNPs with ancestral alleles on the I1 level and no derived SNPs. Probably a false positive for the downstream SNP that defines I1a1a4a1a1b2.

    For OBKR_117_d Germany_EBA_Lech I or I2a1a1a1a1a1a2a or I1a1b1a4a1a1, we're fairly sure that this is not I1 due to negative for five I1 level SNPs and no positive SNPs on the I1 level - the L258 result likely a false positive (one read).

    Some of these samples (I10899/Car1, SF11, BAL051) have a have a mixture of positive and negative calls for SNPs on the I1 level, so I've been calling these ones as pre-I1 (after the split from I2, before the TMRCA of modern I1 individuals) rather than I1.
    I checked SZ20. There isn't a single derived snp call at R or any downstream snp. As I said I've used Reich-lab datastes for these assignments and I think their works are more reliable than Amorim et al.
    As for I1282 and OBKR_117_d, those were false positives and I corrected their haplogroups.

    Quote Originally Posted by Nibelung View Post
    Just discovered that German Bell Beaker sample I6481 you claim to be L392/L1026? Seriously doubt it unless there's a relation to Bolshoy. No offense. Anybody know the autosomal profile?
    I checked I6481. This sample has a limited number of called snps and this particular derived snp call (N1a1a1a1a:CTS3103/Z1954) is probably a false positive.

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    Quote Originally Posted by Kristiina View Post
    According to the paper, Yumin is a female:

    Yumin – The Yumin archaeological site is located in Huade County, Ulanqab city, Inner Mongolia Autonomous Region of China. Yumin culture is the earliest Neolithic culture found in Inner Mongolia thus far. Radiocarbon analysis of charcoal samples associated with the remains of a house were dated to ~8,400 cal BP (62). We sequenced a single individual (M1) from this site, identified to be female, and she was directly radiocarbon dated to 8,415-8,335 cal BP.

    Yumin data.PNG
    According to the paper, it's a female but in the published dataset it's been designated as unknown (U).
    I added a sentence and explained that it's probably a female.

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    Quote Originally Posted by kolgeh View Post
    I've used a stochastic search algorithm (something like penalized optimization) to reduce probability of error and of course some of these assignments are erroneous but haplogroup assignment for ancient samples is prone to error because of nature of data.
    Distinguishing different samples based on coverage, * calls and ... is a great idea but it needs a devoted person who doesn't have any job and other works to do.
    I guess, all of us are non-professionals here.
    But results with so many errors are anyway of little use.

    Generally, I would say that excluding cases with very low coverage its easy to understand for a human which is the correct haplogroup, after just looking at a list of SNPs.
    I guess it is possible to tune the search algorithm to get better results, of course if you have time...

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    Quote Originally Posted by artemv View Post
    I guess, all of us are non-professionals here.
    But results with so many errors are anyway of little use.

    Generally, I would say that excluding cases with very low coverage its easy to understand for a human which is the correct haplogroup, after just looking at a list of SNPs.
    I guess it is possible to tune the search algorithm to get better results, of course if you have time...
    I corrected some of the errors. They're not perfect but they're definitely better than original publications.

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  13. #47
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    Quote Originally Posted by kolgeh View Post
    I7722 Pakistan_H_SaiduSharif_o R2a2b1b2a
    I7722 is derived for Z29272 and Y1379 (R2a2b1b2a1a - YFull: R-Y1376), ancestral for everything under R2a2b1b2a1a1 which was covered in the BAM file (YFull: R-Y1383) and derived for Z29271 (mixed reads, but the positive reads had significantly larger MAPQ) and Z29264 (pre-R2a2b1b2a1a1 - YFull: R-Z29271).

    I7722 also shares two private variants (FT67423 and FGC2051 - the latter is present in a lot of haplogroups, but not anywhere under F-M89 according to YFull at least) and likely one novel variant with NA20887 who himself is also R-Z29271 (xY1383), just like I7722 is. (Novel coordinates (hg38)-ANS-DER: 24348163-C-T - This position only has one read from the I7722 BAM file, and this read has three mismatches from the reference - this may or may not be a false positive, although the fact that NA20887 has it and three other Z29271+ kits I have access to do not have it suggests to me that this result in the data for I7722 seems more likely to be true - one of the mismatches has a much lower base quality than the other two, so this read could effectively be treated as having two mismatches, where one of them is false and the other one is likely to be true).
    Last edited by aaronbee2010; 06-04-2020 at 03:51 AM.
    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

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  15. #48
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    Hmmm Tianyuan is quite strange...
    + for 5/6 K snps, so K for sure
    + for 1/1 K2 - tentatively K2
    + for 1/1 K2b - tentatively K2b
    - for 2/2 NO
    - for 21/21 NO1 - definitely not NO1
    + for 4/25 O - but 4 out of 25 seems quite high to be chance, contamination?
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    Sample I5441 England_C_EBA R1b1a1b1a1a2a7, is this reliable? This would make sample I5441 DF27 which is difficult to pin down. Thanks.

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    Quote Originally Posted by Webb View Post
    Sample I5441 England_C_EBA R1b1a1b1a1a2a7, is this reliable? This would make sample I5441 DF27 which is difficult to pin down. Thanks.
    R1b1a1b1a1a2a7:A12032/S24844 i.e. 22901108 is a C to T snp so it's prone to dna damage but upstream snps are all derived so it might be really R1b1a1b1a1a2a7.

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