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Thread: Ancient I-M253 samples list

  1. #381
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    Quote Originally Posted by JonikW View Post
    I see what you mean after looking at YFull. It seems to have a wider distribution than most. What's your theory on your own Y6228? Could it have spread out from somewhere in the Saxony region, moving south with the Lombards as well as other Germanic tribes, with some heading to Italy over time but others to France, England and up into Scandinavia?
    It looks like Z63 is as widely distributed as I1a1 and I1a2, but I guess it's generally less common and smaller compared to them especially towards the north, I1a2 more so Northwest and I1a1 more so Scandinavia and the Baltic. As you can see that pattern on the ftdna haplotree for example. And you can't be too certain about a lot of the European regions distribution because the number of testers is small and the likelyhood of sample bias. But if it's any indication that's what it looks like. But the most confusing part to me is why it's so freakin small compared to I1a1 and I1a2 in Scandinavia? It's like 20 times or more less common in Sweden, Norway and Findland and maybe a little less in Denmark but they're not testing as much, still it looks about 10 times less common there lol.
    As far as who spread it around I have no idea it could be a bunch of different groups of people. The Y6228 is as widespread as Z63 and you can't really pinpoint its origin or biggest distribution to any region. I would guess Germany and surrounds but again not enough testers too small numbers etc.

    Probably wasn't spread by Vikings though haha.

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  3. #382
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    I've started to add the samples from the "Population genomics of the Viking world" preprint to the Haplogroup I1 Ancient Samples Map. This will take some time as there's a lot of them - there are more than three times as many new samples as there was on there before.

    Can't really add anything additional (such as what's on there in the samples from other papers) from a Y-DNA perspective until the BAM files are available, but can at least put them on the map with the haplogroup designation reported in the preprint and some summary context about the sample - the supplementary data for the preprint is rather informative and worth reading in that regard.

    So far added the I-YSC0000261, I-Z140, I-P109 and I-Z2041 samples.

    I also added the urm035 and urm045 from Sigtuna on there as well. Analysis not complete but enough to go on there as a work in progress.
    Last edited by deadly77; 07-18-2019 at 11:21 PM.

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  5. #383
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    I1 Z140+ A21912+

    Wales England Cornwall Scotland Ireland Normandie
    Quote Originally Posted by deadly77 View Post
    Hopefully my reply to JonikW in #379 above differentiates the two. But it means they didn't intentionally exclude Z63 (or other SNPs) from their assay.
    Are they likely to have gleaned everything possible from the 1x to 2x samples using the shotgun method or is there more to be learned by looking at the SNPs as I've seen you do in the past?
    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
    Mother's Y: traces to Llanvair Discoed, Wales

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  7. #384
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    Quote Originally Posted by JonikW View Post
    Are they likely to have gleaned everything possible from the 1x to 2x samples using the shotgun method or is there more to be learned by looking at the SNPs as I've seen you do in the past?
    No - it appears that they used a program called YLeaf to do the Y-DNA assignments, so they're using software to automate the output of the Y-DNA results rather than manually review the BAM. I've seen this software as well as other similar ones referenced by researchers in some of earlier papers that I've looked at. The preprint authors also add "restricting our analysis to 26,083 biallelic SNPs from the ISOGG (International Society of Genetic Genealogy) 2019 database" in the second supplementary information file.

    The ISOGG tree is rather less comprehensive and behind the trees that YFull and FTDNA use. So the authors are using a less complete reference tree, and their own supplementary information states that they're using a subset of the SNPs that are in the ISOGG tree - ie, not the full ISOGG tree.

    I'm not sure how the YLeaf software accepts or rejects SNP calls. For example, if there's less than 5 reads, does it reject the SNP as not read? Less than 2? What about if there's 9 derived reads and 1 ancestral? Does it pick up one read SNPs? Does it have quality control to monitor the adjacent positions to see if there's a high level of mutation in that region? Will it accept a downstream SNP if an upstream SNP is not read (ie. Z140+ but Z60 no call)? I don't know the answer to any of these but I can anticipate a lot of circumstances where automated software will miss things.

    So a combination of a less comprehensive reference tree and an automated software Y-DNA analysis. I'm pretty confident I'd be able to find more information by manually reviewing the BAM file and I probably have a better understanding of the I1 subclades. It just takes me longer to get through it than a computer. The main barrier to me is gaps in the data from lower quality samples, so I can't make a difference in that regard. But I believe I can make a better assignment in regard to reviewing the raw data that is there - that's been the case with a lot of the samples from other papers.

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  9. #385
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    I was curious if Sigtuna 84005 has a read at position 19318850 ref is T , C = FGC12562

    I tried finding the file at ena but was lost

    When the data was available I was going to check VK291 in the new paper at biorivix. That sample is Z74 * as well.

  10. #386
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    Quote Originally Posted by C.Goodell View Post
    I was curious if Sigtuna 84005 has a read at position 19318850 ref is T , C = FGC12562

    I tried finding the file at ena but was lost

    When the data was available I was going to check VK291 in the new paper at biorivix. That sample is Z74 * as well.
    I had a look in the BAM file but there is no read at 19318850. Coverage is a bit patchy in this one - 1.03x according to the paper. When I was looking into the BAM file there were lots of no calls and all the calls I found were one or two reads.

    Derived SNPs: Z74 1T, Z75 2A, CTS1793 1C, CTS2208 1A, CTS4791 1G, Y2562 2C, Y2565 1C, Y20288 1A

    Ancestral SNPs: Y31675 1C, Y38726 1A, FGC8782 1T, Z135 1C, Y20595 2G, Y20594 2G, Y24701 1C, Y24703 1T, CTS7676 1A, Y2566 2A, L813 1A, Z720 1A

    No call SNPs: CTS5476, Y2561, Y2560, Y2567, Y2563, Y20287, Y20593, Y20289, Y20596, FGC60542, Y24702, Y24704, Y24705, Y24706, Y24707, Y29654, CTS12194, CTS9167, Z718, CTS9364, FGC9478.

    The BAM file for 84005 can be found here: https://www.ebi.ac.uk/ena/data/view/ERS2540884 - click on "BAM File 1" under "Submitted Files (FTP)" - it's 2.98GB so shoudln't take too long to download, based on your connection.

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  12. #387
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    Thanks

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  14. #388
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    Quote Originally Posted by deadly77 View Post
    No - it appears that they used a program called YLeaf to do the Y-DNA assignments, so they're using software to automate the output of the Y-DNA results rather than manually review the BAM. I've seen this software as well as other similar ones referenced by researchers in some of earlier papers that I've looked at. The preprint authors also add "restricting our analysis to 26,083 biallelic SNPs from the ISOGG (International Society of Genetic Genealogy) 2019 database" in the second supplementary information file.

    The ISOGG tree is rather less comprehensive and behind the trees that YFull and FTDNA use. So the authors are using a less complete reference tree, and their own supplementary information states that they're using a subset of the SNPs that are in the ISOGG tree - ie, not the full ISOGG tree.

    I'm not sure how the YLeaf software accepts or rejects SNP calls. For example, if there's less than 5 reads, does it reject the SNP as not read? Less than 2? What about if there's 9 derived reads and 1 ancestral? Does it pick up one read SNPs? Does it have quality control to monitor the adjacent positions to see if there's a high level of mutation in that region? Will it accept a downstream SNP if an upstream SNP is not read (ie. Z140+ but Z60 no call)? I don't know the answer to any of these but I can anticipate a lot of circumstances where automated software will miss things.

    So a combination of a less comprehensive reference tree and an automated software Y-DNA analysis. I'm pretty confident I'd be able to find more information by manually reviewing the BAM file and I probably have a better understanding of the I1 subclades. It just takes me longer to get through it than a computer. The main barrier to me is gaps in the data from lower quality samples, so I can't make a difference in that regard. But I believe I can make a better assignment in regard to reviewing the raw data that is there - that's been the case with a lot of the samples from other papers.
    I’m looking forward to your future BAM analysis. Maybe there’s hope that I share more SNPs downstream of I-Z2041 and I-Z2040 with those 4 samples
    I1> DF29> Z58> Z59> Z2041> Z2040> Z382> S26361> S16414> FGC24354> FGC24357> FGC24356> S10350> FGC75802> Y125947> S21197> BY149414> BY188003> BY188570

    YFull id: YF15884

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  16. #389
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    Quote Originally Posted by deadly77 View Post
    No - it appears that they used a program called YLeaf to do the Y-DNA assignments, so they're using software to automate the output of the Y-DNA results rather than manually review the BAM. I've seen this software as well as other similar ones referenced by researchers in some of earlier papers that I've looked at. The preprint authors also add "restricting our analysis to 26,083 biallelic SNPs from the ISOGG (International Society of Genetic Genealogy) 2019 database" in the second supplementary information file.

    The ISOGG tree is rather less comprehensive and behind the trees that YFull and FTDNA use. So the authors are using a less complete reference tree, and their own supplementary information states that they're using a subset of the SNPs that are in the ISOGG tree - ie, not the full ISOGG tree.

    I'm not sure how the YLeaf software accepts or rejects SNP calls. For example, if there's less than 5 reads, does it reject the SNP as not read? Less than 2? What about if there's 9 derived reads and 1 ancestral? Does it pick up one read SNPs? Does it have quality control to monitor the adjacent positions to see if there's a high level of mutation in that region? Will it accept a downstream SNP if an upstream SNP is not read (ie. Z140+ but Z60 no call)? I don't know the answer to any of these but I can anticipate a lot of circumstances where automated software will miss things.

    So a combination of a less comprehensive reference tree and an automated software Y-DNA analysis. I'm pretty confident I'd be able to find more information by manually reviewing the BAM file and I probably have a better understanding of the I1 subclades. It just takes me longer to get through it than a computer. The main barrier to me is gaps in the data from lower quality samples, so I can't make a difference in that regard. But I believe I can make a better assignment in regard to reviewing the raw data that is there - that's been the case with a lot of the samples from other papers.
    I'm wary of the automated Y-calling software ever since the Central/South Asia paper came out, I looked through the Y-calls file for that paper for fun and there were a fair number of inconsistencies yet the program still considered single positive reads as legitimate despite 10+ negative reads.

    Anyway, I saw the ancient I1 Google map and noticed you had added more pins. It's nice to see the map gain some more locations. This paper is loaded with I1, it's nice to see this finally.
    Last edited by spruithean; 07-20-2019 at 12:44 AM.

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  18. #390
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    Quote Originally Posted by spruithean View Post
    I'm wary of the automated Y-calling software ever since the Central/South Asia paper came out, I looked through the Y-calls file for that paper for fine and there were a fair number of inconsistencies yet the program still considered single positive reads as legitimate despite 10+ negative reads.

    Anyway, I saw the ancient I1 Google map and noticed you had added more pins. It's nice to see the map gain some more locations. This paper is loaded with I1, it's nice to see this finally.
    It's a pleasure to see deadly77's map filling out. I wasn't expecting to see any additions this quickly so thanks to deadly as well as spruithean for pointing it out. I hope those Z140s in particular will be pushed a little further downstream in a few months' time.
    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
    Mother's Y: traces to Llanvair Discoed, Wales

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