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Thread: Ancient I-M253 samples list

  1. #81
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    Yeah, the sample qualities in the Iceland study were of varying quality and I believe they mentioned this in the study. It's better than no data at all, so I'll take the I-M253 with no subclades predictions! I believe the ancient I1 list needs to be updated anyway to include a few additions.

    That U106 list is impressive, it certainly makes the I1 list look rather... bleak. It's quite clear just going through Quiles Indo-European paper that I1 is rather sparse in aDNA lists, the maps in that work certainly show this and the information for I1 is only a few paragraphs compared to the pages of R1b and R1a data.

    Oh well, we just have to keep our eyes peeled for new I1 results from the 4 studies JonikW mentioned. We have to run into more ancient I1 eventually.

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  3. #82
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    Quote Originally Posted by spruithean View Post
    It seems so, I1 populations obviously would have not been able to "avoid" R1b (or even R1a) populations, considering the proximity and likely syncretism.
    Yeah, the I1 carriers were probably part of a SHG forager population before R1a and R1b showed up in Scandinavia. Although it's now safe to say that R1a Z284 and L664 were part of the Corded Ware populations, the question remains when R1b-U106 and some specific subclades of R1b-P312 like L238 arrived in Scandinavia. Corded Ware, Bell Beakers, Unetice and unknown Steppe derived are candidates at the moment for the source imo. We know that U106 was present before 2000 BC in Scandinavia, but it's uncertain which population this sample was part of.

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  5. #83
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    Quote Originally Posted by Radboud View Post
    Yeah, the I1 carriers were probably part of a SHG forager population before R1a and R1b showed up in Scandinavia. Although it's now safe to say that R1a Z284 and L664 were part of the Corded Ware populations, the question remains when R1b-U106 and some specific subclades of R1b-P312 like L238 arrived in Scandinavia. Corded Ware, Bell Beakers, Unetice and unknown Steppe derived are candidates at the moment for the source imo. We know that U106 was present before 2000 BC in Scandinavia, but it's uncertain which population this sample was part of.
    Yep sounds about right... my focus is on U106 naturally and considering what I know and looking at my google doc (so strictly based on known and established data) - we only have three samples that are from Bronze Age (or near enough):

    c. 2275-2032 BC, Battle Axe (2800 - 2300 B.C.)/Nordic LN (2200 - 1800 B.C.), Lille Beddinge 56 - Grave 49, Lilla Bedinge, Sweden, RISE 98, U106 > Z2265+ > BY30097- (FGC36477+)

    c. 2200-1700 BC, Early Unetice, Prague-Jinonice “Zahradnictvķ”, Prague 5 – Jinonice, Czech Republic, I7196, U106 > Z381 > Z156 > Z304 > DF98 > S1911 > S1894

    c. 1881–1646 calBCE, Early Bronze Age, 1900-1700 B.C., De Tuithoorn, Oostwoud, Noord-Holland (West Frisia), I4070, U106 > Z381

    My sub group of DF98 and S1911 > S1894 (I share that with Dr. Iain) would look to be Unetice and I suspect we moved to Northern Germany with the spread of Unetice (and descendant cultures) West and North... hence our association with House of Wettin via Thuringia (but really we need samples from that area to confirm even more).

    The next is the Roman gladiators - and then a bunch of Germanic migration burials... so really we need many more middle to late BA and Iron Age (Jastorf or even just samples from Northern Germany from the late B.C. times) to sort this stuff out. As far as overall for U106 at least - Z18 and especially L48 are very Germanic (Dr. Iain already noted ans assumed that based on pre-aDNA data) and Z156 seems more Rhineland or Western/SW Germanic... once again we need more samples from those population centers along the Rhine - in this map you can see the spread of DF98 in modern testers... Screenshot 2018-10-07 14.12.48.png
    Y-DNA: 4th GGF Adam Weaver born 1785 in Pennsylvania (most likely Rhineland German) - Sergeant, US 17th Inf, War of 1812: R1b-U106-DF98-S1911-S1894/S1900-S4004/FGC14818/FGC14823-FGC14816/FGC14817 shared with 6drif-3 - one of the "Headless" Roman Gladiator/Soldiers!

    mtDNA: 3rd GGM Bridget O'Danagher b. 1843 Lorrha/Dorrha, Ireland - T2b2b - Pagan Migrant Icelander SSG-A3 (grave 4) - Sķlastašir in Eyjafjaršarsżsla, North Iceland is T2b2b.

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  7. #84
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    Double post
    Last edited by Bollox79; 10-07-2018 at 11:55 PM.
    Y-DNA: 4th GGF Adam Weaver born 1785 in Pennsylvania (most likely Rhineland German) - Sergeant, US 17th Inf, War of 1812: R1b-U106-DF98-S1911-S1894/S1900-S4004/FGC14818/FGC14823-FGC14816/FGC14817 shared with 6drif-3 - one of the "Headless" Roman Gladiator/Soldiers!

    mtDNA: 3rd GGM Bridget O'Danagher b. 1843 Lorrha/Dorrha, Ireland - T2b2b - Pagan Migrant Icelander SSG-A3 (grave 4) - Sķlastašir in Eyjafjaršarsżsla, North Iceland is T2b2b.

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  9. #85
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    Ok, after the analysis of SBT-A1's BAM file proved fruitful and we have a fairly good idea where he fits on the phylogenetic tree, I decided to take a look at one of the other I1 samples from the Ancient Icelandic Genomes paper.

    The next one I looked at was SVK-A1 - he was listed as I1b in the Y-DNA column of their report. That looks like it corresponds to I-Z131 in terminology that I'm more comfortable with. The majority of I1 lineages are I1a/DF29+ (>99%) so thought this one might be interesting.

    SVK-A1's BAM file is not as big as the one I downloaded for SBT-A1 (5GB vs. 15G, and looking for the SNP Z131, yep SVK-A1 is positive for that one, although it's only one read for that location. Then I looked for some of the downstream SNPs below Z131 - lots of no calls, but also quite a few negatives for SNPs defining subclades downstream of I-Z131. Again, a fair few of these were one read SNPs but a few were two or three read negative, which I have a bit more confidence in.

    So after getting nowhere with the I1b/Z131 SNPs, I decided to check and make sure that SVK-A1 was actually DF29-. He's a no call for DF29, but there are five other SNPs that are phyloequivalent to DF29 that no one has split off from the main branch yet. SVK-A1 is a no call for CTS9857, but then it lights up with positive results for the other SNPs - Z2892 (10G reads), Z2890 (6A reads), Z2893 (7A reads).

    So I'm pretty sure that SVK-A1 is actually I1a rather than I1b and the one read result for Z131 (which probably led to SVK-A1 being listed as I1b) is a false positive.

    I'll dig in a bit more into SVK-A1's BAM file and see if I can figure out where he is downstream of I-DF29.

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  11. #86
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    Huh, not sure why 15 gigabytes got auto-corrected to a smiley with shades on, but oh well.. not by design...

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  13. #87
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    Ok, I believe that SVK-A1 is down the pathway I1->I-DF29->I-Z2336->I-L22->I-P109->I-S10200->I-FGC21685.

    He's positive with one read for the following SNPs: Y3549, S25633, P109, Y5840, Y5836, FGC21685. He's also positive with two reads for S10891 and S10200 on that branch pathway.

    This puts SVK-A1 at I-FGC21682 on the YFull tree and the FTDNA haplotree. SVK-A1 is a no call for FGC21682 itself, but positive (albeit with one read) for the currently phyloequivalent SNP FGC21685, and a no call for Y20204. It's entirely possible that SVK-A1 is FGC21682- and would split up the phyloequivalent SNPs on the known tree. SVK-A1 is negative for downstream SNPs Y20203, FGC21687, FGC21690 (all one read) and Y20205 (10 reads).

    Given the large number of one reads (and that Z131 was a one read false positive), I wouldn't say this is 100%, but with a large number of these SNPs pointing in the right direction and a couple of them with more than one read, I'm reasonably confident with putting SVK-A1 as for sure I-P109, I-S10200 and I-Y5834, and quite likely I-FGC21685.

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  15. #88
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    Quote Originally Posted by deadly77 View Post
    Ok, I believe that SVK-A1 is down the pathway I1->I-DF29->I-Z2336->I-L22->I-P109->I-S10200->I-FGC21685.

    He's positive with one read for the following SNPs: Y3549, S25633, P109, Y5840, Y5836, FGC21685. He's also positive with two reads for S10891 and S10200 on that branch pathway.

    This puts SVK-A1 at I-FGC21682 on the YFull tree and the FTDNA haplotree. SVK-A1 is a no call for FGC21682 itself, but positive (albeit with one read) for the currently phyloequivalent SNP FGC21685, and a no call for Y20204. It's entirely possible that SVK-A1 is FGC21682- and would split up the phyloequivalent SNPs on the known tree. SVK-A1 is negative for downstream SNPs Y20203, FGC21687, FGC21690 (all one read) and Y20205 (10 reads).

    Given the large number of one reads (and that Z131 was a one read false positive), I wouldn't say this is 100%, but with a large number of these SNPs pointing in the right direction and a couple of them with more than one read, I'm reasonably confident with putting SVK-A1 as for sure I-P109, I-S10200 and I-Y5834, and quite likely I-FGC21685.
    Excellent work and it also confirms that we shouldn't take the assignments as fact in some studies. Well done.
    Living DNA's former Cautious mode:
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    Cornwall: 8%
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    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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  17. #89
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    Quote Originally Posted by JonikW View Post
    Excellent work and it also confirms that we shouldn't take the assignments as fact in some studies. Well done.
    Cheers - these are quite fun and I'll continue to work through the rest of the I1 samples. Although HSJ-A1's BAM file is a bit of a monster at 55.5GB and that is taking a while to download. The flip side of that is there may be quite a bit of good data associated with HSJ-A1.

    Agreed - we shouldn't take summaries at face value. I can see why they did it though, with the one read result for Z131+. Not all one reads are wrong - the F2642+ in the earlier genome of SBT-A1 was also a one read, but there is additional corroboration in the reads of additional SNPs to have more confidence in that one, while there isn't in the Z131+ for SVK-A1.

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  19. #90
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    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

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