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Thread: Ancient I-M253 samples list

  1. #201
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    Quote Originally Posted by deadly77 View Post
    Okay, I've been through 311 SNPs that are in the big I1 block - BAL051 has reads for 33 of these SNPs, so there is a lot of no calls where the position has no reading. Some of that is going to be down to the methodology of the test (the 1240K SNP Capture) and some of it may be due to the age of the sample - it's older than any of the other ones we've discussed in this thread. However, those 33 SNPs (10.6% of the 311 I1 SNPs) have more read SNPs in BAL051 individually than the four RISE samples from Allentoft 2015 combined.

    Derived calls for 13 SNPs: Z2699/FGC2430 (2C), Z2751/L841/YSC0000257, Z2885, Z2887, CTS7751/Z2813, Z2812/CTS7652, Z2860, L124/S64, CTS4532/Z2777, Z2724/V1771 (2G), FGC2441 (2G), CTS10140/Z2837.
    Ancestral calls for 20 SNPs: Z2886, Z2679/CTS136, Z2727, Z2850, Y1962 (4T), P40, Z2747, FGC2422/Z2715, CTS3506/Z2765, FGC33327, CTS11534/Z2871, Y1863/S107/FGC2426, L848/Z2877 /YSC0000299 (2C), FGC2433, Y1950, FGC2427/Z2713, Y1932/S2007, Z2870/CTS11526, S22865/Z2845, Z2806/CTS6765.
    All above one read unless otherwise noted.
    I'm not familiar with that Allentoft 2015, what kind of I1 are those identified as, and what is the age and location of those samples? If you don't mind me asking.

  2. #202
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    Quote Originally Posted by ADW_1981 View Post
    Although this far west is interesting. It might lend support that a survivor moved into the north and succeeded to a culture like Ahrensburg and later to something like TRB.
    Somebody did, that's for sure, regardless of whether this man's line died out. Don't know if it's just me but I'm frustrated with the lack of ancient I1 progress recently. We need some meaningful samples in a good solid paper.
    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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  4. #203
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    Quote Originally Posted by ADW_1981 View Post
    Although this far west is interesting. It might lend support that a survivor moved into the north and succeeded to a culture like Ahrensburg and later to something like TRB.
    That could only lend support for a nice fictional story, maybe a plot of a good movie thriller. Because there's absolutely no concrete evidence for it.

  5. #204
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    Quote Originally Posted by Username View Post
    Cool avatar Raiden Tesla nice!
    But how do you know for sure that it's definitely a dead lineage. Isn't it possible hypothetically that some of those I* people could be direct living descendants?
    Hypothetically yes, but if such lineage indeed existed I think it would turn up somewhere by now.

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  7. #205
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    Quote Originally Posted by Username View Post
    That could only lend support for a nice fictional story, maybe a plot of a good movie thriller. Because there's absolutely no concrete evidence for it.
    Not really. You think it's Bosnian I bet. That's even funnier. There's a lot of support that the I1 progenitor was among HG in Denmark and northern Germany.
    YDNA: R1b-Z220 (A7066+) (1800's Stepney, London(Bethnal Green), UK George Wood b. 1782
    maternal-grandfather YDNA: prob. I1 Gurr, George 1843, Feversham, Kent, England.
    maternal-grandmother YDNA: R1b-P311+ Beech, John Richard b. 1780, Lewes, England
    maternal-ggrandfather YDNA R1b-U106 Thomas, Edward b 1854, Sittingbourne, Kent
    paternal-ggf YDNA: R1b-L48. Gould, John Somerset England 1800s.
    paternal-ggf YDNA: R1b-L48. Scott, William Hamilton mdka Ireland(?) < 1800s

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  9. #206
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    Quote Originally Posted by Username View Post
    I'm not familiar with that Allentoft 2015, what kind of I1 are those identified as, and what is the age and location of those samples? If you don't mind me asking.
    It's a paper that was published in Nature a few years ago titled "Population genomics of Bronze Age Eurasia" and includes a lot of samples - paper is here https://www.nature.com/articles/nature14507 although I'm not sure if it it is public access but you can get some of the supplementary information there, although you can probably get the main paper from Research Gate at https://www.researchgate.net/publica...ze_Age_Eurasia

    Four of the RISE samples from Sweden in this study are often quoted on various blogs and forum posts as being examples of the earliest I1 samples. I'm not so convinced because of the quality and coverage observed in these samples - the data is very poor. For example, RISE207 was positive for a single SNP in the I1 block (and a one-read positive call at that) and no call for all the rest of the 311 SNPs. All of the RISE samples from the Allentoft paper are no call for >97% of the SNPs that define the I1 haplogroup. This makes it difficult to say if they are ancestors of I1 men living today or an extinct lineage. Not enough data. At least with BAL051 and Stora Förvar 11 (SF11) we can call some of the I1 SNPs as ancestral and they're pre-I1 rather than I1. I went through the SNP analysis of the RISE samples in post #131 on this thread.

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  11. #207
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    Quote Originally Posted by ADW_1981 View Post
    Not really. You think it's Bosnian I bet. That's even funnier. There's a lot of support that the I1 progenitor was among HG in Denmark and northern Germany.
    Calm down there gambler lol now you're just being a clown. My point was simply that there is no smoking gun evidence to support yours or any type of theory for origins of I1 at this point. Learn to take a joke without resorting to ad homs and butthurtness. Since you brought up Bosnia and I never did even remotely, I'd like to ask are you an expert on Bosnian history and archeology by any chance?

  12. #208
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    Quote Originally Posted by deadly77 View Post
    It's a paper that was published in Nature a few years ago titled "Population genomics of Bronze Age Eurasia" and includes a lot of samples - paper is here https://www.nature.com/articles/nature14507 although I'm not sure if it it is public access but you can get some of the supplementary information there, although you can probably get the main paper from Research Gate at https://www.researchgate.net/publica...ze_Age_Eurasia

    Four of the RISE samples from Sweden in this study are often quoted on various blogs and forum posts as being examples of the earliest I1 samples. I'm not so convinced because of the quality and coverage observed in these samples - the data is very poor. For example, RISE207 was positive for a single SNP in the I1 block (and a one-read positive call at that) and no call for all the rest of the 311 SNPs. All of the RISE samples from the Allentoft paper are no call for >97% of the SNPs that define the I1 haplogroup. This makes it difficult to say if they are ancestors of I1 men living today or an extinct lineage. Not enough data. At least with BAL051 and Stora Förvar 11 (SF11) we can call some of the I1 SNPs as ancestral and they're pre-I1 rather than I1. I went through the SNP analysis of the RISE samples in post #131 on this thread.
    Oh that's what that is, yes I'm familiar with it. Thanks for the informative rundown, it was more than I asked for, much appreciated.

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    I’m guessing that as millions of more I1 men get tested someone will break up that 312 SNP bottleneck.

    Maybe this is a stupid question but if the current living I1 folks who are not positive for I-DF29 don’t have all 312 SNPs tested, isn’t it possible that one of them might split the bottleneck. How many of these 312 SNPs are actually tested in most next generation tests such as Big Y-500? Are we sure that all of the the
    I-Z17954 folks are positive for all 312 SNPs? What about the two folks on Yfull that are negative for I-DF29 and
    I-Z17954?

    Lastly, in my opinion there needs to be new classifications for ancient samples like the ones mentioned in Iberia, Hungary, and Sweden. Labeling these samples as I* or I1 is misleading.

    Thanks deadly77 for your hard work and expertise. I’m learning more about “I1” from you than from most academic blowhards or nextgen testing companies.

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  16. #210
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    Quote Originally Posted by mwauthy View Post
    I’m guessing that as millions of more I1 men get tested someone will break up that 312 SNP bottleneck.

    Maybe this is a stupid question but if the current living I1 folks who are not positive for I-DF29 don’t have all 312 SNPs tested, isn’t it possible that one of them might split the bottleneck. How many of these 312 SNPs are actually tested in most next generation tests such as Big Y-500? Are we sure that all of the the
    I-Z17954 folks are positive for all 312 SNPs? What about the two folks on Yfull that are negative for I-DF29 and
    I-Z17954?

    Lastly, in my opinion there needs to be new classifications for ancient samples like the ones mentioned in Iberia, Hungary, and Sweden. Labeling these samples as I* or I1 is misleading.

    Thanks deadly77 for your hard work and expertise. I’m learning more about “I1” from you than from most academic blowhards or nextgen testing companies.
    Cheers - I try and follow the real data when I can - there's a fair bit of conjecture out there. Some is good, some not so good... Going back to the primary data such as BAM files is always worth doing if that's an available option.

    As far as I'm aware, no one has yet broken up the I1 bottleneck yet. It's entirely possible that someone will at some point, but if they have and have tested, I'm not aware. There are a few individuals of rare lineages on the DF29- branches. There was some crowdfunding on the I1 Facebook page a couple of years ago for testing one of the individuals with a YElite that is now in the I-CTS12798 branch (DF29-, Z17954-) in the hope that he would break up the I1 block but he didn't show up as confirmed negative for any of them - he was positive for ~270 of them with the remainder being no calls.

    But all possible - in the last couple of years within I-Z140 we had a couple of guys test Z140+/Z141- and then another broke up several of the phyloequivalent SNPs on the I-F2642/S2169 branch which caused a bit of a reordering of the tree. But I thought if someone would break up the I1 block, would have found them by now. Wait and see, I guess.

    You can see how many in your own Big Y test are covered if you go to your YFull homepage and click on YReport on the left hand menu - it will open a new window and the SNPs will be colour-coded on the YReport - green for confirmed positive, red for negative, yellow for ambiguous, grey for no call (the grey is a little harder to read since it is not too diferent from the green colour). I don't have a Big Y myself to look at but I have a FGC YElite - this has three ambiguous calls and 38 no calls in the big I1 block. That's not too bad and comparable to the I-CTS12798 individual mentioned above. I also have a 30x WGS which gets almost everything - zero no calls in the big I1 block and two ambiguous calls. I'd expect that a Big Y Y500 would have less coverage than both of these and a Big Y Y700 to be similar to the YElite.

    I know for sure there are several WGS of I1 folks down the I-DF29 branch. I assume that the ambiguous and no calls in the Y-enrichment tests like Big Y are inferred positive. I guess they could be verified for sure with a Sanger test at YSEQ. I have no idea about the I-Z17954 branch and I think the two folks at I-CTS12798 are a Big Y and a YElite. But most people probably don't look at that part of their results as they are more concerned with their terminal branch and novel variants.

    I agree that the using the I1 label for ancient samples like this is rather misleading - unfortunately they have been quoted as such many, many times and most people reference the blog posts and secondary analysis rather than the primary data. For several of those samples, the lack of data makes it impossible to assign with certainty. I try calling them pre-I1 but I'm not sure if that's appropriate either as it implies that they are an ancestor of modern I1 while to me it's not clear if they are an intermediate or a dead lineage. Not enough data to confirm or disconfirm.

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