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Thread: Ancient I-M253 samples list

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    Back to the Y-DNA... I went through the BAM file for another one of the ancient Icelanders, this time HSJ-A1. The BAM file for this one was significantly larger than any of the other I1 samples - it's 55GB, so that took a fairly long time to download to my computer (which is a bit old and not the fastest). These BAM files were taking up a fair bit of space on my hard drive, so started storing them on an external hard drive to free up some space.

    Anyway, the bigger BAM file for HSJ-A1 lead to a lot of good reads on his genome, so the greatest confidence about these assignments out of any of the ancient Icelanders so far. The positive SNPs for this one are multi-read, often between 10 and 25 reads, and some as high as 37 with much better coverage and less no calls. This one could probably go on the YFull tree.

    The Science 2018 paper has HSJ-A1 as I1a1b3b which would be I-L813. Analysis of the BAM file confirms that, with 10 positive reads for L813 itself, coupled with positive reads for most of the phyloequivalent SNPs for that branch - Z718+, CTS9346+, Z270+ while FGC9478 is a no call.

    Moving on to the subclades, HSJ-A1 is I-Y5476+ (25A, as well as one read for phyloequivalent SNP FGC9465) -> I-Y5483+ (14T) -> I-Y13039+ (14G, as well as Y13504+ from 33G/1A).

    I-Y13039 is as far as HSJ-A1 goes on the YFull tree - HSJ-A1 is negative for all of the downstream subclades on the YFull tree - M10140, Y30042, Y16704, Y8943.

    On FTDNA's haplotree, there are some branches below I-Y13039 that are not on the YFull tree. HSJ-A1 is I-Y111864+ with 10C reads. FTDNA's haplotree has a phyloequivalent SNP Y83756 which HSJ-A1 is negative for Y83756 with 12A reads, so HSJ-A1 splits that branch up. HSJ-A1 is also negative for all the SNPs listed on the I-BY42253 branch downstream of I-Y111864 on FTDNA's haplotree.

    So, HSJ-A1 is I-Y13039 on YFull tree, I-Y111864 on FTDNA's haplotree.

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  3. #92
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    Quote Originally Posted by deadly77 View Post
    There's also a fair bit of discussion in the Science 2018 paper about other data associated with the ancient Icelandic genomes. For example, they mention that the ratio of strontium isotopes measured from the dental enamel can be used to class the samples as migrants or non-migrants, with the latter described in the paper as individuals who spent their first six years of life in Iceland. Both SBT-A1 and SVK-A1 fall into this category of non-migrants.

    However, since the archaeological date for the majority of the samples is described as <1000 CE (and 14C dating for SVK-A1 agrees with <1050 CE) and the settling of Iceland was between 870-930 CE, there can't have been a lot of generations between the birth of the non-migrants in Iceland (such as SBT-A1 ad SVK-A1) and the settling of their ancestors in Iceland from wherever they cam from. There is a fair bit of discussion of autosomal DNA in the Science 2018 paper - they categorise the samples into "Norse" and "Gaelic".

    SVK-A1 is rather more on the "Norse" side compared to "Gaelic" in their interpretation (see Fig 2B and 2C in the paper) compared to most of the other samples, and seems close to contemporary Norway on the PCA in Fig 2A. While I don't want to fully tie autosomal DNA in with Y-DNA haplogroups, looking at the genetic neighbourhood of I-P109 that SVK-A1 would fall in, I-Y5834 and I-FGC21682 at YFull, the distribution is largely Norway among the modern testers, with a few Sweden and one Ireland.

    SBT-A1 then trends closer to what they are describing as "Gaelic" than "Norse" in Fig 2B and 2C, and he seems to fit in rather well with their reference for contemporary England in the PCA in Fig 2A. The modern I-Z140+ testers in the FTDNA project the British Isles (and especially England) are by far the largest population, although that's more likely due to significant population growth once they arrived in the British Isles rather than originating there. Still, given the dating, I guess we can rule out the Normans as an origin for SBT-A1
    Hello Deadly77,

    Great work as usual! From your experience looking into these matters, do you know if these Bam files are available?

    AED249 > I1 L840
    STR486 > I1 L840
    STR241 > I1 L840

    Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria

    Many modern European states trace their roots back to a period known as the Migration Period that spans from Late Antiquity to the early Middle Ages. We have conducted the first population-level analysis of people from this era, generating genomic data from 41 graves from archaeological sites in present-day Bavaria in southern Germany mostly dating to around 500 AD. While they are predominantly of northern/central European ancestry, we also find significant evidence for a nonlocal genetic provenance that is highly enriched among resident Early Medieval women, demonstrating artificial skull deformation. We infer that the most likely origin of the majority of these women was southeastern Europe, resolving a debate that has lasted for more than half a century.

    http://www.pnas.org/content/early/2018/03/06/1719880115
    Known Paper Trail: 45.3% English, 29.7% Scottish, 12.5% Irish, 6.25% German & 6.25% Italian. Or: 87.5% British Isles, 6.25% German & 6.25% Italian.
    LivingDNA: 88.1% British Isles (59.7% English, 27% Scottish & 1.3% Irish), 5.9% Europe South (Aegian 3.4%, Tuscany 1.3%, Sardinia 1.1%), 4.4% Europe NW (Scandinavia) & 1.6% Europe East, (Mordovia).
    FT Big Y: I1-Z140 branch I-F2642 >Y1966 >Y3649 >A13241 >Y3647 >A13248 (circa 930 AD) >A13242/YSEQ (circa 1075 AD) >A13243/YSEQ (circa 1660 AD).

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    Quote Originally Posted by JMcB View Post
    Hello Deadly77,

    Great work as usual! From your experience looking into these matters, do you know if these Bam files are available?

    AED249 > I1 L840
    STR486 > I1 L840
    STR241 > I1 L840

    Population genomic analysis of elongated skulls reveals extensive female-biased immigration in Early Medieval Bavaria

    Many modern European states trace their roots back to a period known as the Migration Period that spans from Late Antiquity to the early Middle Ages. We have conducted the first population-level analysis of people from this era, generating genomic data from 41 graves from archaeological sites in present-day Bavaria in southern Germany mostly dating to around 500 AD. While they are predominantly of northern/central European ancestry, we also find significant evidence for a nonlocal genetic provenance that is highly enriched among resident Early Medieval women, demonstrating artificial skull deformation. We infer that the most likely origin of the majority of these women was southeastern Europe, resolving a debate that has lasted for more than half a century.

    http://www.pnas.org/content/early/2018/03/06/1719880115
    Cheers JMcB - these are quite fun to work through, although each one takes me a bit of time. It's easier if I know what I'm looking for or the coverage is decent. Although with some of these samples I think we pretty much have to take what we can get.

    I had a look at the European Nucleotide Archive for the BAM files that you mentioned - that's where I have been getting the BAM files from the ancient Icelanders.

    AE249 is there, the BAM says it's hg19 and 992MB, which is a little smaller than SVK-A1. Link: https://www.ebi.ac.uk/ena/data/view/ERS1979363
    STR486 is there, the BAM says it's hg19 and 1.5GB. Link: https://www.ebi.ac.uk/ena/data/view/ERS1979393
    STR241 is there, the BAM says it's hg19 and 633MB. Link: https://www.ebi.ac.uk/ena/data/view/ERS1979382

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    Quote Originally Posted by deadly77 View Post
    Cheers JMcB - these are quite fun to work through, although each one takes me a bit of time. It's easier if I know what I'm looking for or the coverage is decent. Although with some of these samples I think we pretty much have to take what we can get.

    I had a look at the European Nucleotide Archive for the BAM files that you mentioned - that's where I have been getting the BAM files from the ancient Icelanders.

    AE249 is there, the BAM says it's hg19 and 992MB, which is a little smaller than SVK-A1. Link: https://www.ebi.ac.uk/ena/data/view/ERS1979363
    STR486 is there, the BAM says it's hg19 and 1.5GB. Link: https://www.ebi.ac.uk/ena/data/view/ERS1979393
    STR241 is there, the BAM says it's hg19 and 633MB. Link: https://www.ebi.ac.uk/ena/data/view/ERS1979382
    Itís nice to know they have a central data base for many of these files. To be honest, I wasnít sure if their basic call of I1 (L840) was because of coverage issues or a lack of time & resources.
    Known Paper Trail: 45.3% English, 29.7% Scottish, 12.5% Irish, 6.25% German & 6.25% Italian. Or: 87.5% British Isles, 6.25% German & 6.25% Italian.
    LivingDNA: 88.1% British Isles (59.7% English, 27% Scottish & 1.3% Irish), 5.9% Europe South (Aegian 3.4%, Tuscany 1.3%, Sardinia 1.1%), 4.4% Europe NW (Scandinavia) & 1.6% Europe East, (Mordovia).
    FT Big Y: I1-Z140 branch I-F2642 >Y1966 >Y3649 >A13241 >Y3647 >A13248 (circa 930 AD) >A13242/YSEQ (circa 1075 AD) >A13243/YSEQ (circa 1660 AD).

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    Quote Originally Posted by JMcB View Post
    It’s nice to know they have a central data base for many of these files. To be honest, I wasn’t sure if their basic call of I1 (L840) was because of coverage issues or a lack of time & resources.
    Earlier in the thread, Bollox79 said he asked Mike Williamson to take a look at those three Bavarian samples - he said "they are targeted capture sequencing, which only looks at specific locations, rather than the whole genome. There isn't much there." so I guess there would be a difference in these tests compared to the whole genome sequencing that was done on the ancient Icelanders. So in addition to missing regions of the Y chromosome due to sample quality,degredation, etc. the analysis just may not cover the regions of the Y chromosome because they were left out of the scanning.

    Bollox79 said that Mike Williamson's look at the samples showed a two were likely I-DF29 (or phyloquivalent) and the other one was I1 but didn't find anything more than that, although they both said that they weren't that familiar with the haplogroup I phylogenetic tree. I'll take a second look when I have some time to get to it - I'm definitely nowhere near as knowledgeable as Alex Williamson but perhaps I know I1 a little better.

    The smart money says I'll likely end up with the same conclusions due to the limited data captured in targeted screening.

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    Continuing to work through the remaining three I1 samples from the Science 2018 paper about the ancient Icelandic genomes. The remaining BAM files are significantly less data than the first three that I analyzed - the largest one is 1.72GB. Bear in mind this is autosomal as well as Y. For comparison, my 30x WGS from YSEQ is 59GB.

    SSJ-A2 is listed in the paper as I1a3b, which would make him I-Z74. In the BAM file, SSJ-A2 is one read positive for Z74. I looked at SNPs that are in the tree downstream of I-Z74 and SSJ-A2 is a no call for most of them, and negative for CTS5476 (which is phyloequivalent for CTS2208). No call for most of the SNPs under I-L813 that I looked for and negative for Y30373, Y19670, BY3434, Y30042 below I-L813. Despite only the one read for Z74, SSJ-A2 also positive for Y2592 and Y2593 (both phyloequivalent with I-Z2336 branch) ans also positive for Y3549 and CTS6868 along the way, so that all matches up.

    SSG-A3 is just listed as I1. I didn't manage to get much out of this one. It looks like he's at least I-DF29 (like most of I1) with a one read positive for Z2892 and later on he's a one read positive for CTS6868 but a no call for most of the downstream SNPs that I looked at.

    DAV-A9 again just listed as I1. Again it looks like he's at least I-DF29 (like most of I1) with a one read positive for CTS9857 and two positive reads for Z2892. I followed his BAM while I was tracking along with SSJ-A2 and SSG-A3, but nothing positive down those I-Z2336 lines. A few negative SNPs Y44733, Y19670, Y19207, Y18234 along the way. No call for Z58, Z59, Z60, Z140.

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    I was happy to receive an email from Vladimir at YFull regarding the ancient Icelandic samples. He says that 10 of the samples from that paper have sufficient quality that they can be added to the YFull tree. Accordingly, SBT-A1, SVK-A1 and HSJ-A1 are now listed as "analysis in progress" (see attached screenshots).

    SBT-A1 YFull.JPGSVK-A1 YFull.JPGHSJ-A1 YFull.JPG

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    Quote Originally Posted by deadly77 View Post
    I was happy to receive an email from Vladimir at YFull regarding the ancient Icelandic samples. He says that 10 of the samples from that paper have sufficient quality that they can be added to the YFull tree. Accordingly, SBT-A1, SVK-A1 and HSJ-A1 are now listed as "analysis in progress" (see attached screenshots).

    SBT-A1 YFull.JPGSVK-A1 YFull.JPGHSJ-A1 YFull.JPG
    Excellent news and nicely done!
    Known Paper Trail: 45.3% English, 29.7% Scottish, 12.5% Irish, 6.25% German & 6.25% Italian. Or: 87.5% British Isles, 6.25% German & 6.25% Italian.
    LivingDNA: 88.1% British Isles (59.7% English, 27% Scottish & 1.3% Irish), 5.9% Europe South (Aegian 3.4%, Tuscany 1.3%, Sardinia 1.1%), 4.4% Europe NW (Scandinavia) & 1.6% Europe East, (Mordovia).
    FT Big Y: I1-Z140 branch I-F2642 >Y1966 >Y3649 >A13241 >Y3647 >A13248 (circa 930 AD) >A13242/YSEQ (circa 1075 AD) >A13243/YSEQ (circa 1660 AD).

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  17. #99
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    Quote Originally Posted by deadly77 View Post
    I was happy to receive an email from Vladimir at YFull regarding the ancient Icelandic samples. He says that 10 of the samples from that paper have sufficient quality that they can be added to the YFull tree. Accordingly, SBT-A1, SVK-A1 and HSJ-A1 are now listed as "analysis in progress" (see attached screenshots).

    SBT-A1 YFull.JPGSVK-A1 YFull.JPGHSJ-A1 YFull.JPG
    Truly exciting stuff. These must be the first ancient I1 samples to get the YFull treatment. Let's hope there will be more soon.
    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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  19. #100
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    Quote Originally Posted by JonikW View Post
    Truly exciting stuff. These must be the first ancient I1 samples to get the YFull treatment. Let's hope there will be more soon.
    You may be correct - I had a look at the other papers that they include samples from, and a lot of them were haplogroup or region specific. There are I1 samples at YFull from the 1000 Genomes project, the Simons Genome Diversity project and the Sardinians paper, but I think these are all from modern individuals.

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