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Thread: Ancient I-M253 samples list

  1. #121
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    Quote Originally Posted by deadly77 View Post
    It's not that these pre-CE samples are DF29- (or the five phyloequivalent SNPs). It's that they are no call - there is no information to assess whether they are DF29+ or DF29-. In the BAM file at that position it's just blank, so it's a Schrodinger's cat situation. Some of the ancient DNA BAM files have pretty decent coverage - HSJ-A1 and SZ45 for example. Some have less where there's not a lot of information that you can reliably call from looking at the BAM file. The RISE samples are in that latter category. I looked at the RISE samples for a few more of the block of SNPs that make up I1 before it divides into descendant subclades. Out of the 70 SNPs looked at so far, there are only 4 SNPs read across the four samples, and they are all one-read. So that's 4/(4x70)=1.4% of just getting a read on SNPs looked at so far. And none of the four SNPs with a reading are showing up in more than one sample so far.

    I think one major factor is when the analysis was conducted. If you look at the publication dates, all but one of the post-CE samples I've looked are from papers published in 2018. The only one that wasn't was published in 2016. All of the pre-CE samples are from papers published in 2015 or 2014. Probably a bit of difference in the technology of sequencing. Also, the ancient remains have had a lot more time to degrade before they were analyzed.

    It may be that some of the RISE samples are not positive for some of the SNPs in the I1 block and may be an extinct lineage that doesn't have descendants that are alive today (or at least not in any database of modern testers that I'm aware of). In that case, wouldn't expect them to be DF29+. But if it's all no calls or one-read positives or negatives, it may be impossible to say with any certainty. We've seen above that CL63 has a single read negative call for DF29, which is clearly bogus due to a much stronger call for Z63 with 11 positive reads. And then SVK-A1 has a single false positive for Z131+ which saw SVK-A1 assigned as I1b in the paper, but when digging further into the data shows he's actually I-FGC21682 based on stronger SNP reads (and therefore must be Z131-). Isolated single read SNPs for derived or ancestral alleles may not be conclusive as we have examples of them turning up false, so we need to approach such calls with a bit of caution.
    Unless the dna samples are too degraded to run further testing there should be a way to rerun tests on these samples using the latest SNP database. The I1 project alone could fund this testing if cost is an issue. It’s not like there are hundreds of ancient I1 samples to choose from. There are only a handful so the most extensive testing should be performed to glean as much knowledge as possible.

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  3. #122
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    Quote Originally Posted by mwauthy View Post
    Unless the dna samples are too degraded to run further testing there should be a way to rerun tests on these samples using the latest SNP database. The I1 project alone could fund this testing if cost is an issue. It’s not like there are hundreds of ancient I1 samples to choose from. There are only a handful so the most extensive testing should be performed to glean as much knowledge as possible.
    I think degradation has to be a factor in some of them. This is quite clear in the Ebenesersdóttir 2018 paper where they mention that they selected 35 ancient Icelanders for WGS, but only 27 of those passed quality control. And it looks like they were all sequenced WGS by the same technique, but there's a world of difference in the data when looking at the BAM files for the six I1 samples, say between HSJ-A1 and DAV-A9 for example.

    A lot of the papers look like they are different institutions and in that case there's going to be differences in DNA extraction and sequencing. Some specify that they are using SNP capture, some specify WGS (say CL63 versus SZ45 in the Longobard cemetery paper). And the read length, depth, etc. are probably going to be different from study to study. I'm sure that leads to some differences as well.

    Across the eight publications, none of them have deep Y chromosome analysis as the primary focus of the manuscript. In most cases, it's simply an entry in a table or a mentioned in a few sentences in the text, if it's mentioned at all. Most of the discussion tends to be about something else - usually autosomal DNA, comparison with modern populations, archaeology or geographic analysis from strontium isotope ratios. Those subjects all get more discussion than Y-DNA haplogroup in these publications. So perhaps there isn't the motivation among the authors and researchers of these publications for the most extensive testing on the Y chromosome if they get the data that they are more interested in. Given some of the incorrect or ambiguous assignment of some of the reported Y-DNA, I would say it isn't high on their agenda. And I would guess that retesting is also not high on their agenda.

    When you say "The I1 project alone could fund this testing if cost is an issue" are you referring to the I1 project at FTDNA? If so, I'm not aware of the FTDNA I1 project funding ancient DNA tests (or retests) in the past. I know there's a general project fund but I would assume that was for sponsoring DTC tests at FTDNA rather than funding ancient DNA research. Several of the project admins have commented and shown interest in the results when I've shared the analysis of the BAM file, but none of them have brought up retesting or funding that. Or perhaps you're referring to another I1 project? Or are you representing one which is offering funding?

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  5. #123
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    Quote Originally Posted by deadly77 View Post
    I think degradation has to be a factor in some of them. This is quite clear in the Ebenesersdóttir 2018 paper where they mention that they selected 35 ancient Icelanders for WGS, but only 27 of those passed quality control. And it looks like they were all sequenced WGS by the same technique, but there's a world of difference in the data when looking at the BAM files for the six I1 samples, say between HSJ-A1 and DAV-A9 for example.

    A lot of the papers look like they are different institutions and in that case there's going to be differences in DNA extraction and sequencing. Some specify that they are using SNP capture, some specify WGS (say CL63 versus SZ45 in the Longobard cemetery paper). And the read length, depth, etc. are probably going to be different from study to study. I'm sure that leads to some differences as well.

    Across the eight publications, none of them have deep Y chromosome analysis as the primary focus of the manuscript. In most cases, it's simply an entry in a table or a mentioned in a few sentences in the text, if it's mentioned at all. Most of the discussion tends to be about something else - usually autosomal DNA, comparison with modern populations, archaeology or geographic analysis from strontium isotope ratios. Those subjects all get more discussion than Y-DNA haplogroup in these publications. So perhaps there isn't the motivation among the authors and researchers of these publications for the most extensive testing on the Y chromosome if they get the data that they are more interested in. Given some of the incorrect or ambiguous assignment of some of the reported Y-DNA, I would say it isn't high on their agenda. And I would guess that retesting is also not high on their agenda.

    When you say "The I1 project alone could fund this testing if cost is an issue" are you referring to the I1 project at FTDNA? If so, I'm not aware of the FTDNA I1 project funding ancient DNA tests (or retests) in the past. I know there's a general project fund but I would assume that was for sponsoring DTC tests at FTDNA rather than funding ancient DNA research. Several of the project admins have commented and shown interest in the results when I've shared the analysis of the BAM file, but none of them have brought up retesting or funding that. Or perhaps you're referring to another I1 project? Or are you representing one which is offering funding?
    I was just speaking generally. If every I1 project member at Ftdna contributed $10 then that would be over $70,000. I’d be much more willing to contribute money towards ancient I1 dna analysis that applies to us all than to a general fund whereby I’m not sure what it’s exactly being used for or for whom.

    There are only 6 BCE I1 samples. That would be over $10k available per sample.

  6. #124
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    Good news - I received an email back from the YFull team - they agree with my analysis and say they will add SZ45 to the YFull tree in the near future, SZ45 will form a new branch I-FGC21818 below I-FGC21819 with sample YF01673.

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  8. #125
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    Quote Originally Posted by deadly77 View Post
    Good news - I received an email back from the YFull team - they agree with my analysis and say they will add SZ45 to the YFull tree in the near future, SZ45 will form a new branch I-FGC21818 below I-FGC21819 with sample YF01673.
    That's great news. Nice work and a valuable contribution to the I1 tree. Thanks.
    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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  10. #126
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    Awesome!

    I'm also hoping that we find some I1 samples in Eastern Germanic studies. It'd be nice to know if there was any I1 amongst the Gepids, Goths, Vandals, etc.

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  12. #127
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    Quote Originally Posted by spruithean View Post
    Awesome!

    I'm also hoping that we find some I1 samples in Eastern Germanic studies. It'd be nice to know if there was any I1 amongst the Gepids, Goths, Vandals, etc.
    Yes, I'm expecting a lot more Scandinavian I1 aDNA next. Even the modern samples on our Z140 branch suggest as much if you take a close look at YFull. Watch this space...
    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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  14. #128
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    Quote Originally Posted by deadly77 View Post
    Good news - I received an email back from the YFull team - they agree with my analysis and say they will add SZ45 to the YFull tree in the near future, SZ45 will form a new branch I-FGC21818 below I-FGC21819 with sample YF01673.
    As they say on Time Team, brilliant!

    Nice work!
    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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  16. #129
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    I went through the BAM file for Stora Förvar 11 (SF11) and the four RISE samples. These are among some of the lowest coverage Y-DNA BAM files that I have looked at. SF11 is the oldest, and in various forums I often see that it's cited as the earliest example of I1 found in ancient DNA samples. Despite the age of this sample, it appears that SF11 has better coverage than the four RISE samples from the Allentoft study.

    Looked at the 312 SNPs that YFull are using today to define the I1 haplogroup on their tree. Three of the SNPs I couldn't find hg19 position for, so I had to leave these out. All of the ancient DNA BAM files that I have looked at are mapped against hg19 reference. The exceptions are the ancient Icelandic samples which are mapped to hg38.

    However, of these 309 SNPs, only 19 positions have a reading in SF11's BAM file and all but two are one read. SF11 is derived for Z2726(1G), Z2792 (1C), Z2802/CTS6221 (1T), Z2882/YSC0000301 (1C), FGC2433 (1A), Z2805/CTS6629 (1A), CTS1748/Z2749 (1G), Z2683 (1T), Z2731 (1A). SF11 is ancestral for Y1831/FGC2468 (1T), Z2714/FGC2425 (1T), CTS3268/Z7262 (1T), L121/S62 (1A), Z2825/CTS9258 (2G), Z2825/CTS9258 (1C), CTS9845 (1A), Z2804/CTS6547 (2C), Z2690 (1G), FGC7871/Y1906 (1G).

    So that's 9 positive SNPs - all of which are one read- out of 309 (2.9%) and 10 negative SNPs out of 309 (3.2%) as the evidence for SF11 to be I1. Could be argued that SF11 isn't I1 at all - more appropriately described as I*, pre-I1, etc. Most likely an extinct lineage that doesn't have descendants alive today - at least none that have tested in any of the current database. It's impossible to say how far between I and I1 that SF11 sits, given that 94% of the 309 SNPs looked at have no call. Perhaps there's a case for putting some of these SNPs in the I1 block as older than some others, but given all the positive SNPs in this block are only one read, I wouldn't have a lot of confidence in saying that.

    While scanning the BAM, also came across a few SNPs that aren't in any database that I looked at: 16377199 1T (right next to L121), 19100097 1A, 4282847 1T, 4282860 1T as well as a couple that are named as found in other haplogroups: F15054+ (P haplogroup), CTS1547/PF4687 (J haplogroup). The latter could be recurrent SNPs and the former could be private mutations associated with SF11's line. Or they could just be false positive one reads. My hunch is the latter.

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  18. #130
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    BAB5 is pretty easy to cover as there is no BAM file - from looking at Szécsényi-Nagy's 2015 paper here https://royalsocietypublishing.org/d...rspb.2015.0339 and dissertation here [URL="https://publications.ub.uni-mainz.de/theses/frontdoor.ph it appears that the Y-DNA testing on BAB5 comprised of a small number of single Y-SNPs. The only ones reported for the I haplogroup in the supplementary information were positive results for M170 (I) and M253 (I1), then a negative result for M438 (I2):
    BAB5.JPG
    None of the >300 phyloequivalent SNPs that make up the I1 block were tested. Given the date assigned to BAB5, it's before the estimated TMRCA of modern I1 descendants and as is the case for SF11, probably not positive for all of the SNPs that define I1. But no data to analyze to verify.

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