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Thread: Ancient I-M253 samples list

  1. #101
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    Not confined to I1, but while trawling round the interwebs for other stuff, I found this map that some helpful person has compiled to show the locations of ancient DNA, colour coded by time period. Clicking on one of the coloured dots brings up a pop up window with reference and in some cases haplogroup data. Just wish it there was an option to filter by haplogroup as well, but it's pretty neat as is. https://umap.openstreetmap.fr/en/map...837#2/51.0/2.0

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  3. #102
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    Next up, 84005 from the Nunnan cemetery in Sigtuna, Sweden, described recently as I1a1b3 (I-Z74) in the paper "Genomic and Strontium Isotope Variation
    Reveal Immigration Patterns in a Viking Age Town" by Krzewinska et al in Current Biology 2018.

    The BAM file at ENA is hg19 rather than the hg38 in the Icelandic samples. That's ok as IGV has options for using either. But important to bear in mind when looking at SNP psoitions.

    Yes, I-Z74 looks right - 84005 is positive for all the phyloequivalent SNPs on that branch (Z74, Z75, CTS1793). Negative for the SNPs associated with I-L813 or I-M6003 branches. Looks positive for some of the SNPs associated with I-CTS2208 branch - there are 11 phyloequivalent SNPs on that branch at YFull. 84005 is positive for Y2562 with two reads, then one read positive for CTS2208, CTS4791, Y2565. 84005 is also negative for Y21369 (two reads) and Z135 (one read) so my feeling is that 84005 breaks up that branch under I-CTS2208. However, with these low reads, some of the results may be false. The other 5 SNPs on that branch are no call.

    Had a look at the branches under that too. No call for I-FGC60542, negative or no call for the SNPs associated with I-CTS7676 or I-Y24701. It's a bit odd on the other branch - under I-Y20287. Negative with two reads for Y20594 and Y20595, positive with one read for Y20288, no call for the remaining four SNPs on that branch.

    I'm inclined to say that 84005 is at the I-CTS2208 branch and breaks that up (four positive SNPS, two negative SNPs), and the Y20288+ is a false positive one read. But it's a problem to make conclusions without the full data.

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  5. #103
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    Double post
    Last edited by deadly77; 10-19-2018 at 02:37 PM. Reason: Double post

  6. #104
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    NO3423 was reported in a Nature Communications 2016 paper by Martiniano et al titled "Genomic signals of migration and continuity in Britain before the Anglo-Saxons" and it includes nine ancient genomes from Northern Britain - seven from a Roman era York cemetery (six R1b, 1 J2), bookended by earlier Iron-Age (female) and later Anglo-Saxon burials. The latter sample (NO3423) the paper assigns as Y-DNA haplogroup "I-S107" and is from Norton Bishopmill, a Christian cemetery dating to 650-910 AD. They sampled three individuals from the burials of 100 skeletons and selected the best preserved sample, which was NO3423 for study.

    The village of Norton is about 30 miles away from me, so was rather interested in checking this one out.

    In the supplementary material, they say "Due to the low coverage of our samples, 1X was the minimum coverage accepted for polymorphisms to be considered and therefore caution is necessary when interpreting these results, since it is likely that some of the alleles identified result of aDNA damage". I think we're going to see a fair bit of this in ancient DNA analysis, so I we should bear that in mind with all other samples too.

    The analysis that they report in Supplementary Table 10 looks like this - seems that they assigned IJK based on L16, I based on P212 and then I1 based on S107. Not sure what's going on here, but in the table it says the mutation is A->C and they report the sample as 1 G read.
    NO3423 Table 10 Y-Haplogroup.JPG
    I looked at my own results at YFull - I'm I1 and I'm a G at that position, although they list S107 again as A to C, with Y1863/FGC2426 as T to G, and then list all three together in Y report. Seems like an odd criterion for assigning I1, but there you go.
    S107 YFull.JPG

    So, on to NO3423's BAM file, which is available at ENA. This one is 2.84 GB in size and it's a hg19 BAM file. Yes, he's a G for S107, as the paper says. While hunting through the BAM file, I also found a positive two reads for Z2790, which is one of the SNPs in the big block of SNPs defining I1.

    Looking for things that are a bit more interesting, NO3423 is positive for DF29 (2 reads) and phyloequivalent SNP CTS9857, which makes him definitely I1. I can rule out some of the small subclades below DF29 - PH790, FGC155560, Y11205, Y11252 and also one of the larger subclades Z63. For the two other big subclades, NO3423 is a no call for Z58 and Z2336 (as well as phyloequivalent SNPs Y2592 and Y2593). I haven't found anything positive downstream of either Z2336 or Z58 - lots of no calls. However, I can say a few things that NO3423 is probably not.
    Under Z2336, NO3423 negative for M227, Y3603. No call for S6742, L22, CTS11603, Y3603, Y3549, S4767, P109.
    Under Z58, NO3423 negative for Z138, Y128537, Z2041, CTS7362. No call for Z59, Z60, CTS8647, Z62, Y12342, Y22033. No call for Z140, but negative for Z141. Also checked F2642 and L338 and negative for those - so no luck for myself, JonikW, JMcB or Spruithean.
    I'll keep taking a look. I'm guessing that he's positive for something under Z2336 or Z58, but just haven't found it yet.

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  8. #105
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    Double post - seems that a lot of things I'm posting on Anthrogenica recently are coming up duplicate.
    Last edited by deadly77; 10-20-2018 at 10:30 AM. Reason: Double post

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  10. #106
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    Quote Originally Posted by deadly77 View Post
    NO3423 was reported in a Nature Communications 2016 paper by Martiniano et al titled "Genomic signals of migration and continuity in Britain before the Anglo-Saxons" and it includes nine ancient genomes from Northern Britain - seven from a Roman era York cemetery (six R1b, 1 J2), bookended by earlier Iron-Age (female) and later Anglo-Saxon burials. The latter sample (NO3423) the paper assigns as Y-DNA haplogroup "I-S107" and is from Norton Bishopmill, a Christian cemetery dating to 650-910 AD. They sampled three individuals from the burials of 100 skeletons and selected the best preserved sample, which was NO3423 for study.

    The village of Norton is about 30 miles away from me, so was rather interested in checking this one out.

    In the supplementary material, they say "Due to the low coverage of our samples, 1X was the minimum coverage accepted for polymorphisms to be considered and therefore caution is necessary when interpreting these results, since it is likely that some of the alleles identified result of aDNA damage". I think we're going to see a fair bit of this in ancient DNA analysis, so I we should bear that in mind with all other samples too.

    The analysis that they report in Supplementary Table 10 looks like this - seems that they assigned IJK based on L16, I based on P212 and then I1 based on S107. Not sure what's going on here, but in the table it says the mutation is A->C and they report the sample as 1 G read.
    NO3423 Table 10 Y-Haplogroup.JPG
    I looked at my own results at YFull - I'm I1 and I'm a G at that position, although they list S107 again as A to C, with Y1863/FGC2426 as T to G, and then list all three together in Y report. Seems like an odd criterion for assigning I1, but there you go.
    S107 YFull.JPG

    So, on to NO3423's BAM file, which is available at ENA. This one is 2.84 GB in size and it's a hg19 BAM file. Yes, he's a G for S107, as the paper says. While hunting through the BAM file, I also found a positive two reads for Z2790, which is one of the SNPs in the big block of SNPs defining I1.

    Looking for things that are a bit more interesting, NO3423 is positive for DF29 (2 reads) and phyloequivalent SNP CTS9857, which makes him definitely I1. I can rule out some of the small subclades below DF29 - PH790, FGC155560, Y11205, Y11252 and also one of the larger subclades Z63. For the two other big subclades, NO3423 is a no call for Z58 and Z2336 (as well as phyloequivalent SNPs Y2592 and Y2593). I haven't found anything positive downstream of either Z2336 or Z58 - lots of no calls. However, I can say a few things that NO3423 is probably not.
    Under Z2336, NO3423 negative for M227, Y3603. No call for S6742, L22, CTS11603, Y3603, Y3549, S4767, P109.
    Under Z58, NO3423 negative for Z138, Y128537, Z2041, CTS7362. No call for Z59, Z60, CTS8647, Z62, Y12342, Y22033. No call for Z140, but negative for Z141. Also checked F2642 and L338 and negative for those - so no luck for myself, JonikW, JMcB or Spruithean.
    I'll keep taking a look. I'm guessing that he's positive for something under Z2336 or Z58, but just haven't found it yet.
    That's remarkable work. He's the only Anglo-Saxon Y that we have so far and I was frustrated that they only pegged him as I1. Now we know a lot more. Thanks!
    Living DNA Cautious mode:
    South Wales Border-related ancestry: 86.8%
    Cornwall: 8%
    Cumbria-related ancestry: 5.2%
    Y line: Peak District, England. Big Y match: Scania, Sweden; TMRCA 1,280 ybp (YFull);
    mtDNA: traces to Glamorgan, Wales, 18th century. Mother's Y line (Wales): R-L21 L371

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  12. #107
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    I went through the BAM files I1 samples AED246, STR241 and STR486 from the Early Medieval Bavaria PNAS paper 2018 from by Veeramah et al. These were mentioned in another post earlier in this thread. My bet was that I wouldn't get much more out of them than Mike Williamson did when he looked at them.

    AED246 I managed to find a one read positive call for DF29+ and a one read negative call for P109-. Everything else I looked for was a no call.
    STR241 seemed to have the lowest coverage out of this set. Everything I looked for was a no call apart from P109-.
    STR486 looked like it had the most out of this set, but still not a lot to report: Z2891+ and Z2892+ (these are both phyloequivalent with I-DF29), then Y11252-, M227-, Z138-, Z60-, F2642-. No call at a whole lot of other positions.

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  14. #108
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    Fantastic work Deadly!

    I really appreciate you doing this, it is definitely painting the picture of where the ancient I1 samples fit in in the big picture.

    So far it seems the vast majority of them are I-DF29 indeed.
    Y-DNA: I-A14097(Scotland),
    Big Y: I-F2642>Y1966>Y3649>A13241>Y3647>A14097 (1,850 YBP)
    mtDNA: pending (Westeremden, Netherlands)
    Other lines:
    R-M222 x2, R-L21 x2, I-M223, R-S1141, R-U198 & R-U106, mtHg J1c3
    Known ancestry
    Paternal: Britain & Ireland, France and Germany
    Maternal: Netherlands

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  16. #109
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    Quote Originally Posted by spruithean View Post
    Fantastic work Deadly!

    I really appreciate you doing this, it is definitely painting the picture of where the ancient I1 samples fit in in the big picture.

    So far it seems the vast majority of them are I-DF29 indeed.
    Thanks - glad to hear that you guys are interested. And hey, Anthrogenica is back after being down for a while

    Agreed, I'd expect a lot of them to be I-DF29, since the DF29- lineages are pretty rare. Probably fair to say that when I1/I-M253 is discussed, it's mostly actually I-DF29. Estimated TMRCA is so close to I1, it's splitting hairs.

    I actually have more confidence in the samples where I'm reliably able to call DF29 or phyloequivalent SNPs. My original thoughts before getting into this would be that ancient DNA would be a good way of figuring out some of the the 300+ SNPs that define I1 along with M253 among the ancient samples may help break up that block and figure some things out between the formation and TMRCA of I1. But having looked at some of these, I think it's going to be risky to make some determinations on low read or no call SNPs. One of the admins of the I-L22 group at YFull was kind enough to share with me the YReport from HSJ-A1, which saves me looking up all of those SNPs. HSJ-A1 had the best coverage of all the ancient I1's that I've seen so far. The YFull YReport shows HSJ-A1 is a no call for 13 of those SNPs - that's not bad at all. My FGC YElite has no call on 34 of those SNPs and 3 more are ambiguous. Then my 30x WGS reads all of them but two are ambiguous. The majority of ancient DNA samples are lower coverage than this. So I'm happy when I can find at least DF29 - lets me know the missing I1 SNPs can be considered presumed positive.

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  18. #110
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    At least Haplogroup I (and more specifically I1) was mentioned in this blog post at Carlos Quiles blog.

    Here's to finding more I-M253 in 2019.
    Y-DNA: I-A14097(Scotland),
    Big Y: I-F2642>Y1966>Y3649>A13241>Y3647>A14097 (1,850 YBP)
    mtDNA: pending (Westeremden, Netherlands)
    Other lines:
    R-M222 x2, R-L21 x2, I-M223, R-S1141, R-U198 & R-U106, mtHg J1c3
    Known ancestry
    Paternal: Britain & Ireland, France and Germany
    Maternal: Netherlands

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